format-version: 1.2 date: 01:05:2008 21:35 saved-by: mi auto-generated-by: OBO-Edit 1.101 subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_goa "GOA and proteome slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" subsetdef: PANTHERGOslim "GO slim for PANTHER" default-namespace: gene_ontology remark: cvs version: $Revision: 4.429 $ [Term] id: GO:0000003 name: reproduction namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, GOC:isa_complete, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "reproductive physiological process" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0000165 name: MAPKKK cascade namespace: biological_process def: "Cascade of at least three protein kinase activities culminating in the phosphorylation and activation of a MAP kinase. MAPKKK cascades lie downstream of numerous signaling pathways." [GOC:mah, PMID:9561267] subset: PANTHERGOslim synonym: "ERK/MAPK cascade" EXACT [] synonym: "MAP kinase cascade" EXACT [] synonym: "MAP kinase kinase kinase cascade" EXACT [] synonym: "MAPK cascade" EXACT [] synonym: "MAPK signaling" RELATED [] synonym: "MAPK signalling" RELATED [] synonym: "MAPKKK cascade during sporulation (sensu Fungi)" NARROW [] synonym: "MAPKKK cascade during sporulation (sensu Saccharomyces)" NARROW [] xref: Reactome:109869 xref: Reactome:211967 xref: Reactome:221732 xref: Reactome:230313 xref: Reactome:238351 xref: Reactome:244909 xref: Reactome:249802 xref: Reactome:252619 xref: Reactome:255804 xref: Reactome:259197 xref: Reactome:262555 xref: Reactome:268509 xref: Reactome:274234 xref: Reactome:280703 xref: Reactome:286727 is_a: GO:0007242 ! intracellular signaling cascade [Term] id: GO:0000166 name: nucleotide binding namespace: molecular_function def: "Interacting selectively with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose moiety." [GOC:mah, ISBN:0198547684] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005488 ! binding [Term] id: GO:0000228 name: nuclear chromosome namespace: cellular_component def: "A chromosome found in the nucleus of a eukaryotic cell." [GOC:mah] subset: goslim_generic subset: PANTHERGOslim synonym: "nuclear interphase chromosome" NARROW [] is_a: GO:0005694 ! chromosome relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000229 name: cytoplasmic chromosome namespace: cellular_component def: "A chromosome found in the cytoplasm." [GOC:mah] subset: goslim_generic subset: gosubset_prok subset: PANTHERGOslim synonym: "cytoplasmic interphase chromosome" NARROW [] is_a: GO:0005694 ! chromosome [Term] id: GO:0000398 name: nuclear mRNA splicing, via spliceosome namespace: biological_process def: "The joining together of exons from one or more primary transcripts of nuclear messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", ISBN:0879695897] subset: PANTHERGOslim synonym: "mRNA splicing" BROAD [] synonym: "pre-mRNA splicing" BROAD [] xref: Reactome:212002 xref: Reactome:221766 xref: Reactome:238383 xref: Reactome:244938 xref: Reactome:249819 xref: Reactome:255735 xref: Reactome:259129 xref: Reactome:262486 xref: Reactome:274165 xref: Reactome:280638 xref: Reactome:286656 xref: Reactome:288338 xref: Reactome:291782 xref: Reactome:293761 xref: Reactome:72172 is_a: GO:0006397 ! mRNA processing [Term] id: GO:0000739 name: DNA strand annealing activity namespace: molecular_function def: "Facilitates the base-pairing of complementary single-stranded DNA." [GOC:elh] subset: PANTHERGOslim is_a: GO:0003690 ! double-stranded DNA binding is_a: GO:0003697 ! single-stranded DNA binding [Term] id: GO:0000910 name: cytokinesis namespace: biological_process alt_id: GO:0007104 alt_id: GO:0016288 def: "A cellular process resulting in the division of the cytoplasm of a cell and its separation into two daughter cells. Cytokinesis usually occurs after growth, replication, and segregation of cellular components." [GOC:ai] subset: goslim_candida subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:211912 xref: Reactome:221676 xref: Reactome:230265 xref: Reactome:238302 xref: Reactome:244868 xref: Reactome:249758 xref: Reactome:252506 xref: Reactome:259076 xref: Reactome:262434 xref: Reactome:265269 xref: Reactome:268395 xref: Reactome:282835 xref: Reactome:286599 xref: Reactome:68884 is_a: GO:0009987 ! cellular process [Term] id: GO:0001501 name: skeletal development namespace: biological_process def: "The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton)." [GOC:jic, http://www.stedmans.com/] subset: PANTHERGOslim is_a: GO:0048731 ! system development [Term] id: GO:0001525 name: angiogenesis namespace: biological_process def: "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels." [ISBN:0878932453] subset: PANTHERGOslim synonym: "blood vessel formation from pre-existing blood vessels" EXACT [] is_a: GO:0048731 ! system development [Term] id: GO:0001531 name: interleukin-21 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-21 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-21" NARROW [] synonym: "interleukin-21 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0001678 name: cellular glucose homeostasis namespace: biological_process def: "A cellular homeostatic process involved in the maintenance of an internal equilibrium of glucose within a cell or between a cell and its external environment." [GOC:dph, GOC:go_curators, GOC:tb] subset: gosubset_prok subset: PANTHERGOslim synonym: "cell glucose homeostasis" EXACT [GOC:dph, GOC:tb] is_a: GO:0042592 ! homeostatic process [Term] id: GO:0002376 name: immune system process namespace: biological_process def: "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." [GOC:add, GOC:mtg_15nov05] comment: This term was added by GO_REF:0000022. subset: goslim_pir subset: PANTHERGOslim is_a: GO:0008150 ! biological_process [Term] id: GO:0002446 name: neutrophil mediated immunity namespace: biological_process def: "Any process involved in the carrying out of an immune response by a neutrophil." [GOC:add, GOC:mtg_15nov05, ISBN:0781735149 "Fundamental Immunology"] comment: This term was added by GO_REF:0000022. subset: PANTHERGOslim is_a: GO:0006955 ! immune response [Term] id: GO:0002447 name: eosinophil mediated immunity namespace: biological_process def: "Any process involved in the carrying out of an immune response by an eosinophil." [GOC:add, GOC:mtg_15nov05, ISBN:0781735149 "Fundamental Immunology"] comment: This term was added by GO_REF:0000022. subset: PANTHERGOslim is_a: GO:0006955 ! immune response [Term] id: GO:0002504 name: antigen processing and presentation of peptide or polysaccharide antigen via MHC class II namespace: biological_process def: "The process by which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex." [GOC:add, ISBN:0781735149 "Fundamental Immunology", PMID:15531770, PMID:15771591, PMID:16153240] subset: PANTHERGOslim synonym: "peptide or polysaccharide antigen processing and presentation of via MHC class II" EXACT [] is_a: GO:0019882 ! antigen processing and presentation [Term] id: GO:0002560 name: basophil mediated immunity namespace: biological_process def: "Any process involved in the carrying out of an immune response by a basophil." [GOC:add, ISBN:0781735149 "Fundamental Immunology"] subset: PANTHERGOslim is_a: GO:0006955 ! immune response [Term] id: GO:0003008 name: system process namespace: biological_process def: "A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective." [GOC:mtg_cardio] subset: PANTHERGOslim synonym: "organ system process" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0003674 name: molecular_function namespace: molecular_function alt_id: GO:0005554 def: "Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions." [GOC:go_curators] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "molecular function unknown" NARROW [] [Term] id: GO:0003676 name: nucleic acid binding namespace: molecular_function def: "Interacting selectively with any nucleic acid." [GOC:jl] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005488 ! binding [Term] id: GO:0003677 name: DNA binding namespace: molecular_function def: "Interacting selectively with DNA (deoxyribonucleic acid)." [GOC:jl] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "microtubule/chromatin interaction" RELATED [] synonym: "plasmid binding" NARROW [] is_a: GO:0003676 ! nucleic acid binding [Term] id: GO:0003678 name: DNA helicase activity namespace: molecular_function alt_id: GO:0003679 def: "Catalysis of the unwinding of a DNA duplex." [GOC:jl, GOC:mah, http://cancerweb.ncl.ac.uk/] comment: Consider also annotating to the molecular function term 'DNA binding ; GO:0003677'. subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0004386 ! helicase activity [Term] id: GO:0003682 name: chromatin binding namespace: molecular_function def: "Interacting selectively with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: PANTHERGOslim synonym: "lamin/chromatin binding" BROAD [] synonym: "microtubule/chromatin interaction" RELATED [] synonym: "nuclear membrane vesicle binding to chromatin" NARROW [] is_a: GO:0005488 ! binding [Term] id: GO:0003684 name: damaged DNA binding namespace: molecular_function def: "Interacting selectively with damaged DNA." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "DNA repair enzyme" RELATED [] synonym: "DNA repair protein" RELATED [] xref: Reactome:7372 is_a: GO:0003677 ! DNA binding [Term] id: GO:0003688 name: DNA replication origin binding namespace: molecular_function def: "Interacting selectively with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally." [GOC:jl, http://cancerweb.ncl.ac.uk/] subset: gosubset_prok subset: PANTHERGOslim synonym: "ARS binding" NARROW [] is_a: GO:0003677 ! DNA binding [Term] id: GO:0003690 name: double-stranded DNA binding namespace: molecular_function def: "Interacting selectively with double-stranded DNA." [GOC:elh] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003677 ! DNA binding [Term] id: GO:0003697 name: single-stranded DNA binding namespace: molecular_function alt_id: GO:0003698 alt_id: GO:0003699 def: "Interacting selectively with single-stranded DNA." [GOC:elh] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003677 ! DNA binding [Term] id: GO:0003700 name: transcription factor activity namespace: molecular_function alt_id: GO:0000130 def: "The function of binding to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:curators] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003677 ! DNA binding is_a: GO:0030528 ! transcription regulator activity [Term] id: GO:0003712 name: transcription cofactor activity namespace: molecular_function def: "The function that links a sequence-specific transcription factor to the core RNA polymerase II complex but does not bind DNA itself." [PMID:10213677] subset: gosubset_prok subset: PANTHERGOslim synonym: "transcriptional co-regulator" EXACT [] synonym: "transcriptional cofactor activity" EXACT [] is_a: GO:0030528 ! transcription regulator activity [Term] id: GO:0003723 name: RNA binding namespace: molecular_function def: "Interacting selectively with an RNA molecule or a portion thereof." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003676 ! nucleic acid binding [Term] id: GO:0003724 name: RNA helicase activity namespace: molecular_function def: "Catalysis of the unwinding of an RNA helix." [GOC:jl] comment: Consider also annotating to the molecular function term 'RNA binding ; GO:0003723'. subset: gosubset_prok subset: PANTHERGOslim xref: EC:2.7.7.- xref: Reactome:7008 is_a: GO:0004386 ! helicase activity [Term] id: GO:0003729 name: mRNA binding namespace: molecular_function def: "Interacting selectively with pre-messenger RNA (pre-mRNA) or messenger RNA (mRNA)." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003723 ! RNA binding [Term] id: GO:0003735 name: structural constituent of ribosome namespace: molecular_function alt_id: GO:0003736 alt_id: GO:0003737 alt_id: GO:0003738 alt_id: GO:0003739 alt_id: GO:0003740 alt_id: GO:0003741 alt_id: GO:0003742 def: "The action of a molecule that contributes to the structural integrity of the ribosome." [GOC:mah] comment: Note that this term may be used to annotate ribosomal RNAs as well as ribosomal proteins. subset: gosubset_prok subset: PANTHERGOslim synonym: "ribosomal protein" BROAD [] synonym: "ribosomal RNA" RELATED [] is_a: GO:0005198 ! structural molecule activity [Term] id: GO:0003743 name: translation initiation factor activity namespace: molecular_function alt_id: GO:0003744 alt_id: GO:0003745 def: "Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:10611 is_a: GO:0045182 ! translation regulator activity [Term] id: GO:0003746 name: translation elongation factor activity namespace: molecular_function alt_id: GO:0008182 alt_id: GO:0008183 def: "Functions in chain elongation during polypeptide synthesis at the ribosome." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:10616 is_a: GO:0045182 ! translation regulator activity [Term] id: GO:0003747 name: translation release factor activity namespace: molecular_function alt_id: GO:0003748 alt_id: GO:0003749 def: "Involved in catalyzing the release of a nascent polypeptide chain from a ribosome." [ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0045182 ! translation regulator activity [Term] id: GO:0003756 name: protein disulfide isomerase activity namespace: molecular_function def: "Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins." [EC:5.3.4.1] subset: gosubset_prok subset: PANTHERGOslim synonym: "protein cysteine-thiol oxidation" RELATED [] synonym: "protein disulfide-isomerase" BROAD [EC:5.3.4.1] synonym: "protein disulfide-isomerase reaction" EXACT [EC:5.3.4.1] synonym: "protein disulphide isomerase activity" EXACT [] synonym: "S-S rearrangase activity" RELATED [EC:5.3.4.1] xref: EC:5.3.4.1 xref: MetaCyc:5.3.4.1-RXN xref: MetaCyc:DISULISOM-RXN is_a: GO:0016853 ! isomerase activity [Term] id: GO:0003774 name: motor activity namespace: molecular_function def: "Catalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate." [GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003674 ! molecular_function [Term] id: GO:0003777 name: microtubule motor activity namespace: molecular_function def: "Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP)." [GOC:mah, ISBN:0815316194] comment: Consider also annotating to the molecular function term 'microtubule binding ; GO:0008017'. subset: PANTHERGOslim synonym: "axonemal motor activity" NARROW [] synonym: "dynein" BROAD [] synonym: "dynein ATPase activity" NARROW [] synonym: "kinesin" BROAD [] synonym: "kinesin motor activity" NARROW [] synonym: "kinetochore motor activity" NARROW [] is_a: GO:0003774 ! motor activity [Term] id: GO:0003779 name: actin binding namespace: molecular_function def: "Interacting selectively with monomeric or multimeric forms of actin, including actin filaments." [GOC:clt] subset: goslim_generic subset: PANTHERGOslim synonym: "membrane associated actin binding" NARROW [] is_a: GO:0008092 ! cytoskeletal protein binding [Term] id: GO:0003823 name: antigen binding namespace: molecular_function def: "Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", ISBN:0721662544 "Dorland's Illustrated Medical Dictionary"] subset: goslim_pir subset: PANTHERGOslim synonym: "antibody" RELATED [] synonym: "B cell receptor activity" RELATED [] synonym: "immunoglobulin" RELATED [] synonym: "opsonin activity" RELATED [] is_a: GO:0005488 ! binding [Term] id: GO:0003824 name: catalytic activity namespace: molecular_function def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "enzyme activity" RELATED [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0003887 name: DNA-directed DNA polymerase activity namespace: molecular_function alt_id: GO:0003888 alt_id: GO:0003889 alt_id: GO:0003890 alt_id: GO:0003891 alt_id: GO:0003893 alt_id: GO:0003894 alt_id: GO:0003895 alt_id: GO:0008723 alt_id: GO:0015999 alt_id: GO:0016000 alt_id: GO:0016448 alt_id: GO:0016449 alt_id: GO:0016450 alt_id: GO:0016451 alt_id: GO:0016452 alt_id: GO:0019984 def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and primer." [EC:2.7.7.7, ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim synonym: "alpha DNA polymerase activity" NARROW [] synonym: "beta DNA polymerase activity" NARROW [] synonym: "delta DNA polymerase activity" NARROW [] synonym: "deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleic acid duplicase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleic duplicase activity" EXACT [EC:2.7.7.7] synonym: "deoxyribonucleic polymerase I" NARROW [EC:2.7.7.7] synonym: "DNA duplicase activity" EXACT [EC:2.7.7.7] synonym: "DNA nucleotidyltransferase (DNA-directed) activity" EXACT [EC:2.7.7.7] synonym: "DNA polymerase alpha" NARROW [EC:2.7.7.7] synonym: "DNA polymerase beta" NARROW [EC:2.7.7.7] synonym: "DNA polymerase gamma" NARROW [EC:2.7.7.7] synonym: "DNA polymerase I" NARROW [EC:2.7.7.7] synonym: "DNA polymerase II" NARROW [EC:2.7.7.7] synonym: "DNA polymerase III" NARROW [EC:2.7.7.7] synonym: "DNA polymerase V activity" NARROW [] synonym: "DNA replicase activity" EXACT [EC:2.7.7.7] synonym: "DNA-dependent DNA polymerase activity" EXACT [EC:2.7.7.7] synonym: "duplicase" BROAD [EC:2.7.7.7] synonym: "epsilon DNA polymerase activity" NARROW [] synonym: "eta DNA polymerase activity" NARROW [] synonym: "gamma DNA-directed DNA polymerase activity" NARROW [] synonym: "iota DNA polymerase activity" NARROW [] synonym: "kappa DNA polymerase activity" NARROW [] synonym: "Klenow fragment" NARROW [EC:2.7.7.7] synonym: "lambda DNA polymerase activity" NARROW [] synonym: "mu DNA polymerase activity" NARROW [] synonym: "nu DNA polymerase activity" NARROW [] synonym: "sequenase" RELATED [EC:2.7.7.7] synonym: "sigma DNA polymerase activity" NARROW [] synonym: "Taq DNA polymerase" NARROW [EC:2.7.7.7] synonym: "Taq Pol I" NARROW [EC:2.7.7.7] synonym: "Tca DNA polymerase" NARROW [EC:2.7.7.7] synonym: "theta DNA polymerase activity" NARROW [] synonym: "zeta DNA polymerase activity" NARROW [] xref: EC:2.7.7.- xref: EC:2.7.7.7 xref: MetaCyc:DNA-DIRECTED-DNA-POLYMERASE-RXN xref: Reactome:11722 xref: Reactome:11738 xref: Reactome:26112 xref: Reactome:69114 is_a: GO:0016740 ! transferase activity [Term] id: GO:0003896 name: DNA primase activity namespace: molecular_function alt_id: GO:0003897 alt_id: GO:0003898 def: "Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases. Catalyzed by a DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase." [GOC:mah, ISBN:0716720094] subset: gosubset_prok subset: PANTHERGOslim xref: EC:2.7.7.- is_a: GO:0003899 ! DNA-directed RNA polymerase activity [Term] id: GO:0003899 name: DNA-directed RNA polymerase activity namespace: molecular_function alt_id: GO:0000129 def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [EC:2.7.7.6] subset: gosubset_prok subset: PANTHERGOslim synonym: "C ribonucleic acid formation factors" RELATED [EC:2.7.7.6] synonym: "C RNA formation factors" RELATED [EC:2.7.7.6] synonym: "deoxyribonucleic acid-dependent ribonucleic acid polymerase activity" EXACT [EC:2.7.7.6] synonym: "DNA-dependent ribonucleate nucleotidyltransferase activity" EXACT [EC:2.7.7.6] synonym: "DNA-dependent RNA nucleotidyltransferase activity" EXACT [EC:2.7.7.6] synonym: "DNA-dependent RNA polymerase activity" EXACT [EC:2.7.7.6] synonym: "DNA-directed RNA polymerase I activity" NARROW [] synonym: "DNA-directed RNA polymerase II activity" NARROW [] synonym: "DNA-directed RNA polymerase III activity" NARROW [] synonym: "nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed) activity" EXACT [EC:2.7.7.6] synonym: "RNA nucleotidyltransferase (DNA-directed) activity" EXACT [EC:2.7.7.6] synonym: "RNA polymerase I activity" NARROW [EC:2.7.7.6] synonym: "RNA polymerase II activity" NARROW [EC:2.7.7.6] synonym: "RNA polymerase III activity" NARROW [EC:2.7.7.6] synonym: "transcriptase" BROAD [EC:2.7.7.6] xref: EC:2.7.7.6 xref: MetaCyc:DNA-DIRECTED-RNA-POLYMERASE-RXN xref: Reactome:11745 is_a: GO:0016740 ! transferase activity [Term] id: GO:0003909 name: DNA ligase activity namespace: molecular_function def: "Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another; requires an energy source such as ATP or NAD+." [ISBN:0716720094] subset: gosubset_prok subset: PANTHERGOslim xref: EC:6.5.1.- xref: Reactome:12459 is_a: GO:0016874 ! ligase activity [Term] id: GO:0003913 name: DNA photolyase activity namespace: molecular_function def: "Catalysis of the repair of a photoproduct resulting from ultraviolet irradiation of two adjacent pyrimidine residues in DNA." [GOC:mah, PMID:11124949] subset: gosubset_prok subset: PANTHERGOslim xref: EC:4.1.99.- is_a: GO:0016829 ! lyase activity [Term] id: GO:0003916 name: DNA topoisomerase activity namespace: molecular_function alt_id: GO:0009387 def: "Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA." [GOC:mah, PMID:8811192] subset: gosubset_prok subset: PANTHERGOslim xref: EC:5.99.1.- is_a: GO:0003677 ! DNA binding is_a: GO:0016853 ! isomerase activity [Term] id: GO:0003924 name: GTPase activity namespace: molecular_function def: "Catalysis of the reaction: GTP + H2O = GDP + phosphate." [ISBN:0198547684] comment: Consider also annotating to the molecular function term 'GTP binding ; GO:0005525'. subset: gosubset_prok subset: PANTHERGOslim synonym: "ARF small monomeric GTPase activity" NARROW [] synonym: "dynamin GTPase activity" NARROW [] synonym: "heterotrimeric G-protein GTPase activity" NARROW [] synonym: "heterotrimeric G-protein GTPase, alpha-subunit" RELATED [] synonym: "heterotrimeric G-protein GTPase, beta-subunit" RELATED [] synonym: "heterotrimeric G-protein GTPase, gamma-subunit" RELATED [] synonym: "hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement" BROAD [] synonym: "protein-synthesizing GTPase activity" NARROW [] synonym: "protein-synthesizing GTPase activity, elongation" NARROW [] synonym: "protein-synthesizing GTPase activity, initiation" NARROW [] synonym: "protein-synthesizing GTPase activity, termination" NARROW [] synonym: "Rab small monomeric GTPase activity" NARROW [] synonym: "Ran small monomeric GTPase activity" NARROW [] synonym: "Ras small monomeric GTPase activity" NARROW [] synonym: "RHEB small monomeric GTPase activity" NARROW [] synonym: "Rho small monomeric GTPase activity" NARROW [] synonym: "Sar small monomeric GTPase activity" NARROW [] synonym: "signal-recognition-particle GTPase activity" NARROW [] synonym: "small monomeric GTPase activity" NARROW [] synonym: "tubulin GTPase activity" NARROW [] xref: Reactome:12513 is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0003964 name: RNA-directed DNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." [EC:2.7.7.49] subset: gosubset_prok subset: PANTHERGOslim synonym: "deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity" EXACT [EC:2.7.7.49] synonym: "DNA nucleotidyltransferase (RNA-directed) activity" EXACT [EC:2.7.7.49] synonym: "reverse transcriptase activity" EXACT [EC:2.7.7.49] synonym: "revertase activity" RELATED [EC:2.7.7.49] synonym: "RNA revertase activity" EXACT [EC:2.7.7.49] synonym: "RNA-dependent deoxyribonucleate nucleotidyltransferase activity" EXACT [EC:2.7.7.49] synonym: "RNA-dependent DNA polymerase activity" EXACT [EC:2.7.7.49] synonym: "RNA-directed DNA polymerase, group II intron encoded" NARROW [] synonym: "RNA-directed DNA polymerase, transposon encoded" NARROW [] synonym: "RNA-instructed DNA polymerase activity" EXACT [EC:2.7.7.49] synonym: "RT" RELATED [EC:2.7.7.49] xref: EC:2.7.7.49 xref: MetaCyc:RNA-DIRECTED-DNA-POLYMERASE-RXN xref: Reactome:10568 is_a: GO:0016740 ! transferase activity [Term] id: GO:0004016 name: adenylate cyclase activity namespace: molecular_function def: "Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate." [EC:4.6.1.1] subset: gosubset_prok subset: PANTHERGOslim synonym: "3',5'-cyclic AMP synthetase activity" EXACT [EC:4.6.1.1] synonym: "adenyl cyclase activity" EXACT [EC:4.6.1.1] synonym: "adenylyl cyclase activity" EXACT [] synonym: "adenylylcyclase activity" EXACT [EC:4.6.1.1] synonym: "ATP diphosphate-lyase (cyclizing) activity" EXACT [EC:4.6.1.1] synonym: "ATP diphosphate-lyase (cyclizing; 3',5'-cyclic-AMP-forming) activity" EXACT [EC:4.6.1.1] synonym: "ATP pyrophosphate-lyase activity" EXACT [EC:4.6.1.1] synonym: "cAMP generating peptide activity" RELATED [] xref: EC:4.6.1.1 xref: MetaCyc:ADENYLATECYC-RXN xref: Reactome:7056 is_a: GO:0016829 ! lyase activity [Term] id: GO:0004190 name: aspartic-type endopeptidase activity namespace: molecular_function def: "Catalysis of the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides; the optimum reaction pH is below 5 due to an aspartic residue involved in the catalytic process." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "aspartic endopeptidase activity" EXACT [] synonym: "aspartic protease activity" EXACT [] synonym: "aspartyl protease activity" EXACT [] synonym: "carboxyl protease activity" EXACT [] xref: EC:3.4.23 xref: Reactome:1933 is_a: GO:0008233 ! peptidase activity [Term] id: GO:0004383 name: guanylate cyclase activity namespace: molecular_function def: "Catalysis of the reaction: GTP = 3',5'-cyclic GMP + diphosphate." [EC:4.6.1.2] subset: gosubset_prok subset: PANTHERGOslim synonym: "GTP diphosphate-lyase (cyclizing) activity" EXACT [EC:4.6.1.2] synonym: "GTP diphosphate-lyase (cyclizing; 3',5'-cyclic-GMP-forming) activity" EXACT [EC:4.6.1.2] synonym: "guanyl cyclase activity" EXACT [EC:4.6.1.2] synonym: "guanylyl cyclase activity" EXACT [] synonym: "receptor guanylate cyclase activity" NARROW [] xref: EC:4.6.1.2 xref: MetaCyc:GUANYLCYC-RXN is_a: GO:0016829 ! lyase activity [Term] id: GO:0004386 name: helicase activity namespace: molecular_function def: "Catalysis of the unwinding of a DNA or RNA duplex." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that most helicases catalyze processive duplex unwinding. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:7001 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004518 name: nuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684] comment: Consider also annotating to the molecular function term 'nucleic acid binding ; GO:0003676'. subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.1.-.- is_a: GO:0016788 ! hydrolase activity, acting on ester bonds [Term] id: GO:0004520 name: endodeoxyribonuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC:mah, ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim synonym: "endonuclease G activity" NARROW [] xref: Reactome:3136 is_a: GO:0004518 ! nuclease activity [Term] id: GO:0004521 name: endoribonuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks." [GOC:mah, ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim synonym: "endonuclease G activity" NARROW [] is_a: GO:0004518 ! nuclease activity [Term] id: GO:0004529 name: exodeoxyribonuclease activity namespace: molecular_function def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a DNA molecule." [GOC:mah, ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0004518 ! nuclease activity [Term] id: GO:0004532 name: exoribonuclease activity namespace: molecular_function def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of an RNA molecule." [GOC:mah, ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0004518 ! nuclease activity [Term] id: GO:0004553 name: hydrolase activity, hydrolyzing O-glycosyl compounds namespace: molecular_function def: "Catalysis of the hydrolysis of any O-glycosyl bond." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim synonym: "O-glucosyl hydrolase activity" EXACT [] xref: EC:3.2.1 is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0004601 name: peroxidase activity namespace: molecular_function alt_id: GO:0016685 alt_id: GO:0016686 alt_id: GO:0016687 def: "Catalysis of the reaction: donor + H2O2 = oxidized donor + 2 H2O." [EC:1.11.1.7] subset: gosubset_prok subset: PANTHERGOslim synonym: "bacterial catalase-peroxidase activity" NARROW [] synonym: "donor:hydrogen-peroxide oxidoreductase activity" EXACT [EC:1.11.1.7] synonym: "eosinophil peroxidase activity" NARROW [] synonym: "extensin peroxidase" NARROW [EC:1.11.1.7] synonym: "guaiacol peroxidase" NARROW [EC:1.11.1.7] synonym: "heme peroxidase" NARROW [EC:1.11.1.7] synonym: "horseradish peroxidase (HRP)" NARROW [EC:1.11.1.7] synonym: "japanese radish peroxidase" NARROW [EC:1.11.1.7] synonym: "lactoperoxidase activity" NARROW [] synonym: "MPO" RELATED [EC:1.11.1.7] synonym: "myeloperoxidase activity" NARROW [] synonym: "oxyperoxidase activity" EXACT [EC:1.11.1.7] synonym: "peroxidase reaction" EXACT [] synonym: "protoheme peroxidase" NARROW [EC:1.11.1.7] synonym: "pyrocatechol peroxidase" NARROW [EC:1.11.1.7] synonym: "scopoletin peroxidase" NARROW [EC:1.11.1.7] synonym: "thiocyanate peroxidase" NARROW [EC:1.11.1.7] synonym: "verdoperoxidase" NARROW [EC:1.11.1.7] xref: EC:1.11.1.7 xref: MetaCyc:PEROXID-RXN xref: Reactome:4411 is_a: GO:0016209 ! antioxidant activity [Term] id: GO:0004620 name: phospholipase activity namespace: molecular_function def: "Catalysis of the hydrolysis of a glycerophospholipid." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.1.1.- is_a: GO:0016298 ! lipase activity [Term] id: GO:0004645 name: phosphorylase activity namespace: molecular_function def: "Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase." [EC:2.4.1.1] subset: gosubset_prok subset: PANTHERGOslim synonym: "1,4-alpha-D-glucan:phosphate alpha-D-glucosyltransferase activity" EXACT [EC:2.4.1.1] synonym: "1,4-alpha-glucan phosphorylase activity" EXACT [EC:2.4.1.1] synonym: "alpha-glucan phosphorylase" BROAD [EC:2.4.1.1] synonym: "amylopectin phosphorylase" NARROW [EC:2.4.1.1] synonym: "amylophosphorylase activity" NARROW [EC:2.4.1.1] synonym: "glucan phosphorylase" NARROW [EC:2.4.1.1] synonym: "glucosan phosphorylase" NARROW [EC:2.4.1.1] synonym: "granulose phosphorylase" NARROW [EC:2.4.1.1] synonym: "muscle phosphorylase" NARROW [EC:2.4.1.1] synonym: "muscle phosphorylase a and b activity" NARROW [EC:2.4.1.1] synonym: "myophosphorylase" NARROW [EC:2.4.1.1] synonym: "polyphosphorylase activity" EXACT [EC:2.4.1.1] synonym: "potato phosphorylase" NARROW [EC:2.4.1.1] synonym: "starch phosphorylase" NARROW [EC:2.4.1.1] xref: EC:2.4.1.1 xref: MetaCyc:RXN-1826 is_a: GO:0016757 ! transferase activity, transferring glycosyl groups [Term] id: GO:0004672 name: protein kinase activity namespace: molecular_function alt_id: GO:0050222 def: "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP." [MetaCyc:PROTEIN-KINASE-RXN] comment: Note that triphosphate is used as a phosphate donor by at least one kinase. subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "protamine kinase activity" NARROW [] xref: MetaCyc:PROTEIN-KINASE-RXN xref: Reactome:4030 is_a: GO:0016301 ! kinase activity [Term] id: GO:0004675 name: transmembrane receptor protein serine/threonine kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + receptor-protein serine/threonine = ADP + receptor-protein serine/threonine phosphate." [EC:2.7.11.30] subset: PANTHERGOslim synonym: "activin receptor kinase activity" NARROW [EC:2.7.11.30] synonym: "ATP:receptor-protein phosphotransferase activity" EXACT [EC:2.7.11.30] synonym: "receptor protein serine/threonine kinase activity" EXACT [EC:2.7.11.30] synonym: "receptor serine/threonine protein kinase activity" EXACT [EC:2.7.11.30] synonym: "receptor type I serine/threonine protein kinase activity" NARROW [EC:2.7.11.30] synonym: "receptor type II serine/threonine protein kinase activity" NARROW [EC:2.7.11.30] synonym: "STK13" RELATED [EC:2.7.11.30] synonym: "TGF-beta kinase activity" NARROW [EC:2.7.11.30] xref: EC:2.7.11.- xref: Reactome:11160 is_a: GO:0004872 ! receptor activity [Term] id: GO:0004714 name: transmembrane receptor protein tyrosine kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate, to initiate a change in cell activity." [EC:2.7.10.1, GOC:mah] subset: gosubset_prok subset: PANTHERGOslim synonym: "anaplastic lymphoma kinase activity" NARROW [EC:2.7.10.1] synonym: "ATP:protein-L-tyrosine O-phosphotransferase (receptor-type) activity" EXACT [EC:2.7.10.1] synonym: "ATP:protein-tyrosine O-phosphotransferase activity" BROAD [EC:2.7.10.1] synonym: "Drosophila Eph kinase activity" NARROW [EC:2.7.10.1] synonym: "ephrin-B3 receptor tyrosine kinase activity" NARROW [EC:2.7.10.1] synonym: "insulin receptor protein-tyrosine kinase activity" NARROW [EC:2.7.10.1] synonym: "neurite outgrowth regulating kinase activity" NARROW [EC:2.7.10.1] synonym: "neurotrophin TRK receptor activity" RELATED [] synonym: "neurotrophin TRKA receptor activity" RELATED [] synonym: "neurotrophin TRKB receptor activity" RELATED [] synonym: "neurotrophin TRKC receptor activity" RELATED [] synonym: "novel oncogene with kinase-domain activity" NARROW [EC:2.7.10.1] synonym: "receptor protein tyrosine kinase activity" EXACT [EC:2.7.10.1] synonym: "receptor protein-tyrosine kinase activity" EXACT [EC:2.7.10.1] synonym: "sevenless receptor activity" RELATED [] xref: EC:2.7.10.1 xref: Reactome:11064 is_a: GO:0004872 ! receptor activity [Term] id: GO:0004715 name: non-membrane spanning protein tyrosine kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate." [EC:2.7.10.2] subset: PANTHERGOslim synonym: "ATP:protein-L-tyrosine O-phosphotransferase (non-specific) activity" EXACT [EC:2.7.10.2] synonym: "ATP:protein-tyrosine O-phosphotransferase activity" BROAD [EC:2.7.10.2] synonym: "Bruton's tyrosine kinase activity" NARROW [EC:2.7.10.2] synonym: "cytoplasmic protein tyrosine kinase activity" NARROW [EC:2.7.10.2] synonym: "focal adhesion kinase activity" NARROW [EC:2.7.10.2] synonym: "janus kinase 1 activity" NARROW [EC:2.7.10.2] synonym: "janus kinase 2 activity" NARROW [EC:2.7.10.2] synonym: "janus kinase 3 activity" NARROW [EC:2.7.10.2] synonym: "non-specific protein-tyrosine kinase activity" EXACT [EC:2.7.10.2] synonym: "p60c-src protein tyrosine kinase activity" NARROW [EC:2.7.10.2] xref: EC:2.7.10.2 is_a: GO:0004672 ! protein kinase activity [Term] id: GO:0004721 name: phosphoprotein phosphatase activity namespace: molecular_function def: "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity." [EC:3.1.3.16, ISBN:0198547684] subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "phosphoprotein phosphohydrolase activity" EXACT [EC:3.1.3.16] synonym: "protein phosphatase activity" EXACT [] synonym: "protein phosphatase-1 activity" NARROW [EC:3.1.3.16] synonym: "protein phosphatase-2A activity" NARROW [EC:3.1.3.16] synonym: "protein phosphatase-2B activity" NARROW [EC:3.1.3.16] synonym: "protein phosphatase-2C activity" NARROW [EC:3.1.3.16] xref: EC:3.1.3.16 xref: MetaCyc:3.1.3.16-RXN xref: Reactome:1887 is_a: GO:0016791 ! phosphoric monoester hydrolase activity [Term] id: GO:0004801 name: transaldolase activity namespace: molecular_function def: "Catalysis of the reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate." [EC:2.2.1.2] subset: gosubset_prok subset: PANTHERGOslim synonym: "dihydroxyacetone transferase activity" EXACT [EC:2.2.1.2] synonym: "dihydroxyacetonetransferase activity" EXACT [EC:2.2.1.2] synonym: "glycerone transferase activity" EXACT [EC:2.2.1.2] synonym: "sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity" EXACT [EC:2.2.1.2] xref: EC:2.2.1.2 xref: MetaCyc:TRANSALDOL-RXN xref: Reactome:15049 is_a: GO:0016740 ! transferase activity [Term] id: GO:0004802 name: transketolase activity namespace: molecular_function def: "Catalysis of the reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate." [EC:2.2.1.1] subset: gosubset_prok subset: PANTHERGOslim synonym: "glycoaldehyde transferase activity" EXACT [EC:2.2.1.1] synonym: "glycolaldehydetransferase activity" EXACT [EC:2.2.1.1] synonym: "sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glycolaldehydetransferase activity" EXACT [EC:2.2.1.1] xref: EC:2.2.1.1 xref: MetaCyc:1TRANSKETO-RXN xref: Reactome:15050 is_a: GO:0016740 ! transferase activity [Term] id: GO:0004812 name: aminoacyl-tRNA ligase activity namespace: molecular_function def: "Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of pyrophosphate and AMP." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that the bond resulting from this reaction is an carboxylic acid ester bond, linking the alpha carboxyl group of the amino acid to either the 2' or 3' hydroxyl of the 3'- terminal adenyl residue of the tRNA. subset: gosubset_prok subset: PANTHERGOslim synonym: "aminoacyl-tRNA synthetase activity" EXACT [GOC:hjd] xref: EC:6.1.1.- is_a: GO:0016874 ! ligase activity [Term] id: GO:0004842 name: ubiquitin-protein ligase activity namespace: molecular_function alt_id: GO:0004840 alt_id: GO:0004841 def: "Catalysis of the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine." [EC:6.3.2.19, PMID:9635407] subset: gosubset_prok subset: PANTHERGOslim synonym: "E2" NARROW [] synonym: "E3" NARROW [] synonym: "ubiquitin activity" RELATED [EC:6.3.2.19] synonym: "ubiquitin conjugating enzyme activity" EXACT [] synonym: "ubiquitin ligase activity" EXACT [] synonym: "ubiquitin protein ligase activity" EXACT [] synonym: "ubiquitin protein-ligase activity" EXACT [] synonym: "ubiquitin-activating enzyme" EXACT [] synonym: "ubiquitin-conjugating enzyme activity" EXACT [] synonym: "ubiquitin-ligase activity" EXACT [] synonym: "ubiquitin:protein-lysine N-ligase (AMP-forming) activity" EXACT [EC:6.3.2.19] xref: EC:6.3.2.19 xref: MetaCyc:UBIQUITIN--PROTEIN-LIGASE-RXN xref: Reactome:15168 xref: Reactome:15171 is_a: GO:0016874 ! ligase activity [Term] id: GO:0004857 name: enzyme inhibitor activity namespace: molecular_function def: "Stops, prevents or reduces the activity of an enzyme." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0030234 ! enzyme regulator activity [Term] id: GO:0004867 name: serine-type endopeptidase inhibitor activity namespace: molecular_function def: "Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides; a serine residue (and a histidine residue) are at the active center of the enzyme." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "serine protease inhibitor activity" EXACT [] synonym: "serine proteinase inhibitor activity" EXACT [] synonym: "serpin activity" NARROW [] xref: Reactome:15233 is_a: GO:0030414 ! protease inhibitor activity [Term] id: GO:0004869 name: cysteine protease inhibitor activity namespace: molecular_function alt_id: GO:0004870 subset: gosubset_prok subset: PANTHERGOslim synonym: "thiol protease inhibitor" EXACT [] is_a: GO:0030414 ! protease inhibitor activity [Term] id: GO:0004872 name: receptor activity namespace: molecular_function def: "Combining with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:ceb, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "receptor guanylate cyclase activity" NARROW [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0004879 name: ligand-dependent nuclear receptor activity namespace: molecular_function def: "A ligand-dependent receptor found in the nucleus of the cell." [GOC:ai] comment: Note that this term represents a function and not a gene product. Consider also annotating to the molecular function term 'transcription regulator activity ; GO:0030528'. subset: PANTHERGOslim synonym: "nuclear hormone receptor" NARROW [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0004896 name: hematopoietin/interferon-class (D200-domain) cytokine receptor activity namespace: molecular_function subset: PANTHERGOslim is_a: GO:0004872 ! receptor activity [Term] id: GO:0004904 name: interferon receptor activity namespace: molecular_function def: "Combining with an interferon to initiate a change in cell activity." [GOC:ai] subset: PANTHERGOslim is_a: GO:0004896 ! hematopoietin/interferon-class (D200-domain) cytokine receptor activity [Term] id: GO:0004907 name: interleukin receptor activity namespace: molecular_function def: "Combining with an interleukin to initiate a change in cell activity." [GOC:ai] subset: PANTHERGOslim synonym: "IL receptor" EXACT [] is_a: GO:0004896 ! hematopoietin/interferon-class (D200-domain) cytokine receptor activity [Term] id: GO:0004930 name: G-protein coupled receptor activity namespace: molecular_function alt_id: GO:0016526 def: "A receptor that binds an extracellular ligand and transmits the signal to a heterotrimeric G-protein complex. These receptors are characteristically seven-transmembrane receptors and are made up of hetero- or homodimers." [GOC:dph, GOC:tb, IUPHAR:2.0] subset: gosubset_prok subset: PANTHERGOslim synonym: "G protein coupled receptor activity" EXACT [] synonym: "G protein linked receptor activity" EXACT [] synonym: "G-protein coupled receptor activity, unknown ligand" EXACT [] synonym: "G-protein linked receptor activity" EXACT [] synonym: "G-protein-coupled receptor activity" EXACT [] synonym: "GPCR activity" EXACT [] synonym: "orphan G protein coupled receptor activity" EXACT [] synonym: "orphan G-protein coupled receptor activity" EXACT [] synonym: "orphan GPCR activity" EXACT [] xref: Reactome:35 is_a: GO:0004872 ! receptor activity [Term] id: GO:0005024 name: transforming growth factor beta receptor activity namespace: molecular_function def: "Combining with transforming growth factor beta to initiate a change in cell activity." [GOC:mah] subset: PANTHERGOslim synonym: "TGF-beta receptor activity" EXACT [] synonym: "TGFbeta receptor activity" EXACT [] synonym: "TGFbetaR" EXACT [] is_a: GO:0004675 ! transmembrane receptor protein serine/threonine kinase activity [Term] id: GO:0005031 name: tumor necrosis factor receptor activity namespace: molecular_function alt_id: GO:0005032 alt_id: GO:0005033 def: "Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function." [GOC:jl, http://lookwayup.com/] subset: PANTHERGOslim synonym: "NGF/TNF (6 C-domain) receptor activity" NARROW [] synonym: "TNF receptor activity" EXACT [] synonym: "TNF receptor activity, type I" NARROW [] synonym: "TNF receptor activity, type II" NARROW [] synonym: "tumor necrosis factor receptor activity, type I" NARROW [] synonym: "tumor necrosis factor receptor activity, type II" NARROW [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0005083 name: small GTPase regulator activity namespace: molecular_function def: "Modulates the rate of GTP hydrolysis by a small monomeric GTPase." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim synonym: "small GTPase regulatory/interacting protein activity" RELATED [] is_a: GO:0030234 ! enzyme regulator activity [Term] id: GO:0005085 name: guanyl-nucleotide exchange factor activity namespace: molecular_function alt_id: GO:0008433 alt_id: GO:0019839 def: "Stimulates the exchange of guanyl nucleotides by a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase." [GOC:kd, GOC:mah] subset: gosubset_prok subset: PANTHERGOslim synonym: "GEF" EXACT [] synonym: "GNRP" NARROW [] synonym: "guanyl-nucleotide release factor activity" EXACT [] synonym: "guanyl-nucleotide releasing factor" EXACT [] xref: Reactome:11431 is_a: GO:0030234 ! enzyme regulator activity [Term] id: GO:0005102 name: receptor binding namespace: molecular_function def: "Interacting selectively with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "adrenocorticotropin" RELATED [] synonym: "allatostatin" RELATED [] synonym: "insulin" RELATED [] synonym: "receptor ligand" NARROW [] synonym: "receptor-associated protein activity" RELATED [] is_a: GO:0005515 ! protein binding [Term] id: GO:0005125 name: cytokine activity namespace: molecular_function def: "Functions to control the survival, growth, differentiation and effector function of tissues and cells." [ISBN:0198599471] subset: PANTHERGOslim is_a: GO:0005102 ! receptor binding [Term] id: GO:0005126 name: hematopoietin/interferon-class (D200-domain) cytokine receptor binding namespace: molecular_function subset: PANTHERGOslim synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor ligand" NARROW [] is_a: GO:0005125 ! cytokine activity [Term] id: GO:0005132 name: interferon-alpha/beta receptor binding namespace: molecular_function def: "Interacting selectively with the interferon-alpha/beta receptor." [GOC:ai] subset: PANTHERGOslim synonym: "interferon-alpha/beta" NARROW [] synonym: "interferon-alpha/beta receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0005133 name: interferon-gamma receptor binding namespace: molecular_function def: "Interacting selectively with the interferon-gamma receptor." [GOC:ai] subset: PANTHERGOslim synonym: "interferon-gamma" NARROW [] synonym: "interferon-gamma receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0005134 name: interleukin-2 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-2 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-2" NARROW [] synonym: "interleukin-2 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005135 name: interleukin-3 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-3 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-3" NARROW [] synonym: "interleukin-3 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005136 name: interleukin-4 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-4 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-4" NARROW [] synonym: "interleukin-4 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005137 name: interleukin-5 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-5 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-5" NARROW [] synonym: "interleukin-5 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005138 name: interleukin-6 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-6 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-6" NARROW [] synonym: "interleukin-6 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005139 name: interleukin-7 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-7 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-7" NARROW [] synonym: "interleukin-7 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005140 name: interleukin-9 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-9 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-9" NARROW [] synonym: "interleukin-9 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005141 name: interleukin-10 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-10 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-10" NARROW [] synonym: "interleukin-10 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005142 name: interleukin-11 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-11 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-11" NARROW [] synonym: "interleukin-11 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005143 name: interleukin-12 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-12 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-12" NARROW [] synonym: "interleukin-12 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding is_a: GO:0008083 ! growth factor activity [Term] id: GO:0005144 name: interleukin-13 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-13 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-13" NARROW [] synonym: "interleukin-13 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0005145 name: interleukin-14 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-14 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-14" NARROW [] synonym: "interleukin-14 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0005160 name: transforming growth factor beta receptor binding namespace: molecular_function def: "Interacting selectively with the transforming growth factor beta receptor." [GOC:ai] subset: PANTHERGOslim synonym: "activin" RELATED [] synonym: "inhibin" RELATED [] synonym: "TGF-beta receptor binding" EXACT [] synonym: "TGFbeta receptor binding" EXACT [] synonym: "transforming growth factor beta" NARROW [] synonym: "transforming growth factor beta ligand binding to type I receptor" RELATED [] synonym: "transforming growth factor beta ligand binding to type II receptor" RELATED [] synonym: "transforming growth factor beta receptor anchoring activity" RELATED [] synonym: "transforming growth factor beta receptor ligand" NARROW [] xref: Reactome:4078 is_a: GO:0005102 ! receptor binding [Term] id: GO:0005164 name: tumor necrosis factor receptor binding namespace: molecular_function def: "Interacting selectively with the tumor necrosis factor receptor." [GOC:ai] subset: PANTHERGOslim synonym: "TNF receptor binding" EXACT [] synonym: "tumor necrosis factor" NARROW [] synonym: "tumor necrosis factor receptor ligand" NARROW [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0005165 name: neurotrophin receptor binding namespace: molecular_function def: "Interacting selectively with a neurotrophin receptor." [GOC:ai] subset: PANTHERGOslim synonym: "neurotrophin" NARROW [] synonym: "neurotrophin receptor ligand" NARROW [] is_a: GO:0005125 ! cytokine activity [Term] id: GO:0005179 name: hormone activity namespace: molecular_function def: "The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "cAMP generating peptide activity" NARROW [] synonym: "glycopeptide hormone" NARROW [] synonym: "lipopeptide hormone" NARROW [] synonym: "peptide hormone" NARROW [] is_a: GO:0005102 ! receptor binding [Term] id: GO:0005184 name: neuropeptide hormone activity namespace: molecular_function def: "The action characteristic of a neuropeptide hormone, any peptide hormone that acts in the central nervous system. A neuropeptide is any of several types of molecules found in brain tissue, composed of short chains of amino acids; they include endorphins, enkephalins, vasopressin, and others. They are often localized in axon terminals at synapses and are classified as putative neurotransmitters, although some are also hormones." [GOC:mah] subset: PANTHERGOslim synonym: "neurohormone" EXACT [] is_a: GO:0005179 ! hormone activity [Term] id: GO:0005198 name: structural molecule activity namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003674 ! molecular_function [Term] id: GO:0005200 name: structural constituent of cytoskeleton namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of a cytoskeletal structure." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005198 ! structural molecule activity [Term] id: GO:0005201 name: extracellular matrix structural constituent namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the extracellular matrix." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim synonym: "extracellular matrix glycoprotein" NARROW [] is_a: GO:0005198 ! structural molecule activity [Term] id: GO:0005215 name: transporter activity namespace: molecular_function alt_id: GO:0005478 def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells." [GOC:ai, GOC:df] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "small-molecule carrier or transporter" RELATED [] xref: Reactome:1391 is_a: GO:0003674 ! molecular_function [Term] id: GO:0005216 name: ion channel activity namespace: molecular_function def: "Catalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:cy, GOC:mtg_transport, ISBN:0815340729] subset: goslim_generic subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003674 ! molecular_function [Term] id: GO:0005243 name: gap junction channel activity namespace: molecular_function alt_id: GO:0015285 alt_id: GO:0015286 def: "A wide pore channel activity that enables a direct cytoplasmic connection from one cell to an adjacent cell. The gap junction can pass large solutes as well as electrical signals between cells. Gap junctions consist of two gap junction hemi-channels, or connexons, one contributed by each membrane through which the gap junction passes." [GOC:dgh, GOC:mtg_transport, ISBN:0815340729] subset: PANTHERGOslim synonym: "connexin" RELATED [] synonym: "innexin" NARROW [] synonym: "innexin channel activity" EXACT [] synonym: "intercellular channel" BROAD [] is_a: GO:0005216 ! ion channel activity [Term] id: GO:0005244 name: voltage-gated ion channel activity namespace: molecular_function def: "Catalysis of the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons." [GOC:mtg_transport, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim synonym: "voltage gated ion channel activity" EXACT [] synonym: "voltage-dependent ion channel activity" EXACT [] is_a: GO:0005216 ! ion channel activity [Term] id: GO:0005245 name: voltage-gated calcium channel activity namespace: molecular_function alt_id: GO:0010173 def: "Catalysis of the transmembrane transfer of a calcium ion by a voltage-gated channel." [GOC:mtg_transport, GOC:tb, ISBN:0815340729] subset: PANTHERGOslim synonym: "depolarisation-activated calcium channel" BROAD [] synonym: "depolarisation-activated voltage-gated calcium channel" EXACT [] synonym: "depolarization-activated calcium channel" BROAD [] synonym: "depolarization-activated voltage gated calcium channel activity" EXACT [] synonym: "depolarization-activated voltage-gated calcium channel activity" EXACT [] synonym: "voltage gated calcium channel activity" EXACT [] synonym: "voltage-dependent calcium channel activity" EXACT [] synonym: "voltage-gated calcium ion channel activity" EXACT [] synonym: "voltage-sensitive calcium channel" EXACT [] is_a: GO:0005244 ! voltage-gated ion channel activity is_a: GO:0005261 ! cation channel activity [Term] id: GO:0005248 name: voltage-gated sodium channel activity namespace: molecular_function def: "Catalysis of the transmembrane transfer of a sodium ion by a voltage-gated channel." [GOC:mtg_transport, ISBN:0815340729] subset: PANTHERGOslim synonym: "voltage gated sodium channel activity" EXACT [] synonym: "voltage-dependent sodium channel activity" EXACT [] synonym: "voltage-gated sodium ion channel activity" EXACT [] synonym: "voltage-sensitive sodium channel" EXACT [] is_a: GO:0005244 ! voltage-gated ion channel activity is_a: GO:0005261 ! cation channel activity [Term] id: GO:0005249 name: voltage-gated potassium channel activity namespace: molecular_function def: "Catalysis of the transmembrane transfer of a potassium ion by a voltage-gated channel." [GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim synonym: "voltage gated potassium channel activity" EXACT [] synonym: "voltage-dependent potassium channel activity" EXACT [] synonym: "voltage-gated potassium ion channel activity" EXACT [] synonym: "voltage-sensitive potassium channel" EXACT [] is_a: GO:0005244 ! voltage-gated ion channel activity is_a: GO:0005261 ! cation channel activity [Term] id: GO:0005253 name: anion channel activity namespace: molecular_function def: "Catalysis of the energy-independent passage of anions across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005216 ! ion channel activity [Term] id: GO:0005261 name: cation channel activity namespace: molecular_function alt_id: GO:0015281 alt_id: GO:0015338 def: "Catalysis of the energy-independent passage of cations across a lipid bilayer down a concentration gradient." [GOC:def, GOC:dph, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim synonym: "cation diffusion facilitator activity" EXACT [] synonym: "nonselective cation channel activity" EXACT [] is_a: GO:0005216 ! ion channel activity is_a: GO:0008324 ! cation transmembrane transporter activity [Term] id: GO:0005319 name: lipid transporter activity namespace: molecular_function def: "Enables the directed movement of lipids into, out of, within or between cells." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "apolipoprotein" RELATED [] synonym: "high-density lipoprotein" RELATED [] synonym: "lipophorin" NARROW [] synonym: "low-density lipoprotein" RELATED [] synonym: "very-low-density lipoprotein" RELATED [] xref: Reactome:7042 is_a: GO:0005215 ! transporter activity [Term] id: GO:0005326 name: neurotransmitter transporter activity namespace: molecular_function def: "Enables the directed movement of a neurotransmitter into, out of, within or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005215 ! transporter activity [Term] id: GO:0005484 name: SNAP receptor activity namespace: molecular_function alt_id: GO:0005485 alt_id: GO:0005486 def: "Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion." [GOC:mah, PMID:14570579] subset: PANTHERGOslim synonym: "Q-SNARE activity" NARROW [] synonym: "R-SNARE activity" NARROW [] synonym: "SNAP-25" NARROW [] synonym: "SNARE" EXACT [] synonym: "t-SNARE activity" NARROW [] synonym: "v-SNARE activity" NARROW [] is_a: GO:0005515 ! protein binding [Term] id: GO:0005488 name: binding namespace: molecular_function def: "The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "ligand" NARROW [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0005509 name: calcium ion binding namespace: molecular_function def: "Interacting selectively with calcium ions (Ca2+)." [GOC:ai] subset: goslim_generic subset: gosubset_prok subset: PANTHERGOslim synonym: "calcium ion storage activity" RELATED [] is_a: GO:0005488 ! binding [Term] id: GO:0005515 name: protein binding namespace: molecular_function alt_id: GO:0045308 def: "Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "alpha-2 macroglobulin receptor-associated protein activity" RELATED [] synonym: "protein amino acid binding" EXACT [] synonym: "protein degradation tagging activity" RELATED [] synonym: "protein tagging activity" RELATED [] xref: Reactome:6125 is_a: GO:0005488 ! binding [Term] id: GO:0005516 name: calmodulin binding namespace: molecular_function def: "Interacting selectively with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states." [GOC:krc] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005515 ! protein binding [Term] id: GO:0005544 name: calcium-dependent phospholipid binding namespace: molecular_function def: "Interacting selectively with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005488 ! binding [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "cellular component unknown" NARROW [] [Term] id: GO:0005576 name: extracellular region namespace: cellular_component def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators] comment: Note that this term is intended to annotate gene products that are not uniformly attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "extracellular" EXACT [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0005578 name: proteinaceous extracellular matrix namespace: cellular_component def: "A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity." [GOC:mtg_sensu, ISBN:0198547684] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: PANTHERGOslim synonym: "extracellular matrix (sensu Metazoa)" EXACT [] is_a: GO:0031012 ! extracellular matrix [Term] id: GO:0005615 name: extracellular space namespace: cellular_component def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684] comment: Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: PANTHERGOslim synonym: "intercellular space" RELATED [] relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0005618 name: cell wall namespace: cellular_component def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan." [ISBN:0198547684] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0005622 name: intracellular namespace: cellular_component def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "protoplasm" EXACT [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0005634 name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: PANTHERGOslim relationship: part_of GO:0005622 ! intracellular [Term] id: GO:0005635 name: nuclear envelope namespace: cellular_component alt_id: GO:0005636 def: "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." [ISBN:0198547684] subset: goslim_generic subset: goslim_plant subset: PANTHERGOslim relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005654 name: nucleoplasm namespace: cellular_component def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653] subset: goslim_generic subset: goslim_plant subset: PANTHERGOslim relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005694 name: chromosome namespace: cellular_component def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] is_a: GO:0043226 ! organelle [Term] id: GO:0005730 name: nucleolus namespace: cellular_component def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: PANTHERGOslim relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0005737 name: cytoplasm namespace: cellular_component def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim relationship: part_of GO:0005622 ! intracellular [Term] id: GO:0005739 name: mitochondrion namespace: cellular_component def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: PANTHERGOslim synonym: "mitochondria" EXACT [] is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005743 name: mitochondrial inner membrane namespace: cellular_component def: "The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae." [GOC:ai] subset: PANTHERGOslim relationship: part_of GO:0005739 ! mitochondrion [Term] id: GO:0005764 name: lysosome namespace: cellular_component def: "Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_plant subset: PANTHERGOslim is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005768 name: endosome namespace: cellular_component def: "A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: PANTHERGOslim is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005773 name: vacuole namespace: cellular_component def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "vacuolar carboxypeptidase Y" RELATED [] is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005777 name: peroxisome namespace: cellular_component alt_id: GO:0019818 def: "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [ISBN:0815316194] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: PANTHERGOslim synonym: "peroxisome vesicle" BROAD [] is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005783 name: endoplasmic reticulum namespace: cellular_component def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: PANTHERGOslim synonym: "ER" EXACT [] is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005794 name: Golgi apparatus namespace: cellular_component def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: PANTHERGOslim synonym: "Golgi" BROAD [] synonym: "Golgi complex" EXACT [] synonym: "Golgi ribbon" NARROW [] is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005811 name: lipid particle namespace: cellular_component def: "Any particle of coalesced lipids in the cytoplasm of a cell. May include associated proteins." [GOC:mah] comment: Note that this term does not refer to vesicle, but instead to structures in which lipids do not necessarily form bilayers. subset: goslim_generic subset: PANTHERGOslim synonym: "lipid droplet" EXACT [] relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005815 name: microtubule organizing center namespace: cellular_component def: "A region in a eukaryotic cell, such as a centrosome or basal body, from which microtubules grow." [ISBN:0815316194] subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: PANTHERGOslim synonym: "microtubule organising centre" EXACT [] synonym: "MTOC" EXACT [] relationship: part_of GO:0005856 ! cytoskeleton [Term] id: GO:0005829 name: cytosol namespace: cellular_component def: "That part of the cytoplasm that does not contain membranous or particulate subcellular components." [ISBN:0198547684] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0005834 name: heterotrimeric G-protein complex namespace: cellular_component def: "Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G-protein coupled receptors to an effector protein." [ISBN:0198547684] comment: See also the molecular function term 'G-protein coupled receptor activity ; GO:0004930'. subset: gosubset_prok subset: PANTHERGOslim synonym: "heterotrimeric G-protein GTPase activity" RELATED [] synonym: "heterotrimeric G-protein GTPase, alpha-subunit" NARROW [] synonym: "heterotrimeric G-protein GTPase, beta-subunit" NARROW [] synonym: "heterotrimeric G-protein GTPase, gamma-subunit" NARROW [] is_a: GO:0043234 ! protein complex [Term] id: GO:0005840 name: ribosome namespace: cellular_component def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "ribosomal RNA" RELATED [] is_a: GO:0030529 ! ribonucleoprotein complex [Term] id: GO:0005856 name: cytoskeleton namespace: cellular_component def: "Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, ISBN:0198547684, PMID:16959967] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim relationship: part_of GO:0005622 ! intracellular [Term] id: GO:0005874 name: microtubule namespace: cellular_component def: "Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." [ISBN:0879693568] subset: PANTHERGOslim is_a: GO:0005856 ! cytoskeleton [Term] id: GO:0005886 name: plasma membrane namespace: cellular_component def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "bacterial inner membrane" NARROW [] synonym: "cell membrane" EXACT [] synonym: "cytoplasmic membrane" EXACT [] synonym: "inner endospore membrane" NARROW [] synonym: "juxtamembrane" BROAD [] synonym: "plasmalemma" EXACT [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0005921 name: gap junction namespace: cellular_component def: "Any specialized areas of the plasma membranes of adjacent cells where the membranes are 2-4 nm apart and penetrated by a connexon. This gap junction allows passage of small molecules and electric current. The variety in the properties of gap junctions is reflected in the number of connexins, the family of proteins which form the junction." [GOC:mtg_muscle, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "communicating junction" EXACT [] synonym: "macula communicans" EXACT [] synonym: "zonula communicans" EXACT [] is_a: GO:0030054 ! cell junction [Term] id: GO:0005923 name: tight junction namespace: cellular_component def: "A belt-like region of very close contact between the plasma membranes of adjacent cells so that the intercellular space is completely occluded. They occur in epithelia and brain endothelia." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "zonula occludens" EXACT [] is_a: GO:0030054 ! cell junction [Term] id: GO:0005929 name: cilium namespace: cellular_component def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:kva, ISBN:0198547684] subset: goslim_generic subset: goslim_pir subset: PANTHERGOslim is_a: GO:0005575 ! cellular_component [Term] id: GO:0005975 name: carbohydrate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "carbohydrate metabolism" EXACT [] xref: Reactome:211962 xref: Reactome:221727 xref: Reactome:230309 xref: Reactome:238347 xref: Reactome:244905 xref: Reactome:249798 xref: Reactome:252538 xref: Reactome:255716 xref: Reactome:259109 xref: Reactome:262468 xref: Reactome:265303 xref: Reactome:268427 xref: Reactome:274144 xref: Reactome:280617 xref: Reactome:282867 xref: Reactome:286632 xref: Reactome:288323 xref: Reactome:289858 xref: Reactome:290396 xref: Reactome:291760 xref: Reactome:292414 xref: Reactome:293735 xref: Reactome:71387 is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0005976 name: polysaccharide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving polysaccharides, a polymer of more than 10 monosaccharide residues joined by glycosidic linkages." [ISBN:0198547684] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "glycan metabolic process" EXACT [] synonym: "glycan metabolism" EXACT [] synonym: "polysaccharide metabolism" EXACT [] is_a: GO:0005975 ! carbohydrate metabolic process [Term] id: GO:0005977 name: glycogen metabolic process namespace: biological_process def: "The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha(1->4) glycosidic linkage, joined together by alpha(1->6) glycosidic linkages." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "glycogen metabolism" EXACT [] is_a: GO:0005976 ! polysaccharide metabolic process [Term] id: GO:0005984 name: disaccharide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any disaccharide, sugars composed of two monosaccharide units." [GOC:jl, ISBN:01928006X] subset: gosubset_prok subset: PANTHERGOslim synonym: "disaccharide metabolism" EXACT [] is_a: GO:0005975 ! carbohydrate metabolic process [Term] id: GO:0005996 name: monosaccharide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "monosaccharide metabolism" EXACT [] is_a: GO:0005975 ! carbohydrate metabolic process [Term] id: GO:0006091 name: generation of precursor metabolites and energy namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." [GOC:jl] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "energy pathways" BROAD [] synonym: "metabolic energy generation" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0006094 name: gluconeogenesis namespace: biological_process def: "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [http://cancerweb.ncl.ac.uk/] subset: gosubset_prok subset: PANTHERGOslim synonym: "glucose biosynthesis" EXACT [] synonym: "glucose biosynthetic process" EXACT [] xref: MetaCyc:GLUCONEO-PWY xref: Reactome:211959 xref: Reactome:221724 xref: Reactome:230306 xref: Reactome:238346 xref: Reactome:244904 xref: Reactome:249797 xref: Reactome:252537 xref: Reactome:255715 xref: Reactome:259108 xref: Reactome:262467 xref: Reactome:265302 xref: Reactome:268426 xref: Reactome:274143 xref: Reactome:280616 xref: Reactome:282853 xref: Reactome:286631 xref: Reactome:288321 xref: Reactome:289853 xref: Reactome:290391 xref: Reactome:291759 xref: Reactome:292413 xref: Reactome:293734 xref: Reactome:70263 is_a: GO:0005996 ! monosaccharide metabolic process [Term] id: GO:0006096 name: glycolysis namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle." [ISBN:0716720094] subset: gosubset_prok subset: PANTHERGOslim xref: MetaCyc:PWY-1042 xref: Reactome:205678 xref: Reactome:211678 xref: Reactome:215022 xref: Reactome:221449 xref: Reactome:224309 xref: Reactome:230078 xref: Reactome:232889 xref: Reactome:238101 xref: Reactome:241068 xref: Reactome:244707 xref: Reactome:246626 xref: Reactome:249623 xref: Reactome:250880 xref: Reactome:252418 xref: Reactome:253953 xref: Reactome:255579 xref: Reactome:256993 xref: Reactome:258955 xref: Reactome:260605 xref: Reactome:262328 xref: Reactome:263636 xref: Reactome:265175 xref: Reactome:266579 xref: Reactome:268303 xref: Reactome:271266 xref: Reactome:273994 xref: Reactome:277357 xref: Reactome:280474 xref: Reactome:281774 xref: Reactome:282785 xref: Reactome:284467 xref: Reactome:286492 xref: Reactome:288329 xref: Reactome:289846 xref: Reactome:290386 xref: Reactome:290856 xref: Reactome:291697 xref: Reactome:292416 xref: Reactome:292897 xref: Reactome:293675 xref: Reactome:70171 xref: Reactome:70467 is_a: GO:0005996 ! monosaccharide metabolic process [Term] id: GO:0006098 name: pentose-phosphate shunt namespace: biological_process def: "The process by which glucose is oxidized, coupled to NADPH synthesis. Glucose 6-P is oxidized with the formation of carbon dioxide (CO2), ribulose 5-phosphate and reduced NADP; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", MetaCyc:PENTOSE-P-PWY] subset: gosubset_prok subset: PANTHERGOslim synonym: "hexose monophosphate pathway" EXACT [] synonym: "pentose phosphate pathway" EXACT [] synonym: "pentose phosphate shunt" EXACT [] synonym: "pentose-phosphate pathway" EXACT [] xref: MetaCyc:PENTOSE-P-PWY xref: Reactome:211595 xref: Reactome:221371 xref: Reactome:230009 xref: Reactome:238027 xref: Reactome:244643 xref: Reactome:249579 xref: Reactome:252383 xref: Reactome:255538 xref: Reactome:258912 xref: Reactome:262287 xref: Reactome:265141 xref: Reactome:268265 xref: Reactome:273950 xref: Reactome:280429 xref: Reactome:282800 xref: Reactome:286444 xref: Reactome:288225 xref: Reactome:289807 xref: Reactome:290356 xref: Reactome:291674 xref: Reactome:292354 xref: Reactome:293650 xref: Reactome:71336 is_a: GO:0005996 ! monosaccharide metabolic process [Term] id: GO:0006099 name: tricarboxylic acid cycle namespace: biological_process def: "A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "citric acid cycle" EXACT [] synonym: "Krebs cycle" EXACT [] synonym: "TCA cycle" EXACT [] xref: MetaCyc:P102-PWY xref: MetaCyc:P103-PWY xref: MetaCyc:P104-PWY xref: MetaCyc:P105-PWY xref: MetaCyc:P42-PWY xref: MetaCyc:P62-PWY xref: MetaCyc:P63-PWY xref: MetaCyc:P82-PWY xref: MetaCyc:TCA xref: Reactome:211545 xref: Reactome:221322 xref: Reactome:229962 xref: Reactome:237979 xref: Reactome:244598 xref: Reactome:249541 xref: Reactome:252352 xref: Reactome:255507 xref: Reactome:258879 xref: Reactome:262256 xref: Reactome:265143 xref: Reactome:268230 xref: Reactome:273912 xref: Reactome:280391 xref: Reactome:282813 xref: Reactome:286448 xref: Reactome:288227 xref: Reactome:289779 xref: Reactome:290340 xref: Reactome:291646 xref: Reactome:292355 xref: Reactome:293654 xref: Reactome:71403 relationship: part_of GO:0006091 ! generation of precursor metabolites and energy [Term] id: GO:0006109 name: regulation of carbohydrate metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates." [GOC:go_curators] subset: gosubset_prok subset: PANTHERGOslim synonym: "regulation of carbohydrate metabolism" EXACT [] relationship: regulates GO:0005975 ! carbohydrate metabolic process [Term] id: GO:0006118 name: electron transport namespace: biological_process def: "OBSOLETE. The transport of electrons from an electron donor to an electron acceptor." [http://cancerweb.ncl.ac.uk/] comment: This term was obsoleted because it describes a molecular function. To update annotations, use biological_process term 'oxidation reduction ; GO:0055114' and consider biological_process term 'respiratory electron transport chain ; GO:0022904' or its children, biological_process term 'respiratory electron transport chain ; GO:0022904' or its children, and molecular_function term 'oxidoreductase activity ; GO:0016491' or its children. subset: PANTHERGOslim synonym: "6-phosphofructokinase reduction" RELATED [] synonym: "dihydrobiopterin reduction" RELATED [] synonym: "dihydrolipoamide reduction" RELATED [] synonym: "dihydrolipoylprotein reduction" RELATED [] synonym: "dihydropteridine reduction" RELATED [] synonym: "electron transfer" EXACT [] synonym: "other pathways of electron transport" RELATED [] synonym: "oxidized glutathione reduction" RELATED [] synonym: "protein-disulfide reduction" RELATED [] is_obsolete: true [Term] id: GO:0006119 name: oxidative phosphorylation namespace: biological_process def: "The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", ISBN:0471331309 "Biochemical Pathways"] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "respiratory-chain phosphorylation" EXACT [] is_a: GO:0006091 ! generation of precursor metabolites and energy [Term] id: GO:0006124 name: ferredoxin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving ferredoxin, any simple, nonenzymatic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur. Iron and sulfur atoms are present in one or two clusters of two or four atoms of each." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "ferredoxin metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006139 name: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0006144 name: purine base metabolic process namespace: biological_process def: "The chemical reactions and pathways involving purine bases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine." [GOC:go_curators] subset: gosubset_prok subset: PANTHERGOslim synonym: "purine base metabolism" EXACT [] synonym: "purine metabolic process" NARROW [] synonym: "purine metabolism" NARROW [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0006206 name: pyrimidine base metabolic process namespace: biological_process def: "The chemical reactions and pathways involving pyrimidine bases, 1,3-diazine, organic nitrogenous bases." [GOC:go_curators] subset: gosubset_prok subset: PANTHERGOslim synonym: "pyrimidine base metabolism" EXACT [] synonym: "pyrimidine metabolic process" BROAD [] synonym: "pyrimidine metabolism" BROAD [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0006259 name: DNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "DNA metabolism" EXACT [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0006260 name: DNA replication namespace: biological_process def: "The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "DNA biosynthesis" RELATED [] synonym: "DNA biosynthetic process" RELATED [] synonym: "DNA synthesis" RELATED [] xref: Reactome:176101 xref: Reactome:176116 xref: Reactome:176175 xref: Reactome:176187 xref: Reactome:176250 xref: Reactome:176264 xref: Reactome:176298 xref: Reactome:176318 xref: Reactome:204211 xref: Reactome:205947 xref: Reactome:209363 xref: Reactome:210696 xref: Reactome:210713 xref: Reactome:211049 xref: Reactome:211609 xref: Reactome:213204 xref: Reactome:215512 xref: Reactome:219112 xref: Reactome:220587 xref: Reactome:220604 xref: Reactome:220896 xref: Reactome:221383 xref: Reactome:222984 xref: Reactome:224670 xref: Reactome:227905 xref: Reactome:229236 xref: Reactome:229253 xref: Reactome:229565 xref: Reactome:230019 xref: Reactome:231470 xref: Reactome:236114 xref: Reactome:237238 xref: Reactome:238037 xref: Reactome:239451 xref: Reactome:243273 xref: Reactome:244047 xref: Reactome:244652 xref: Reactome:249742 xref: Reactome:252497 xref: Reactome:255670 xref: Reactome:259062 xref: Reactome:262424 is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0006281 name: DNA repair namespace: biological_process def: "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:211856 xref: Reactome:212077 xref: Reactome:221621 xref: Reactome:221835 xref: Reactome:230215 xref: Reactome:230400 xref: Reactome:238255 xref: Reactome:238446 xref: Reactome:244827 xref: Reactome:244986 xref: Reactome:249726 xref: Reactome:249863 xref: Reactome:252611 xref: Reactome:255661 xref: Reactome:255776 xref: Reactome:259050 xref: Reactome:259167 xref: Reactome:262414 xref: Reactome:262525 xref: Reactome:265253 xref: Reactome:265355 xref: Reactome:268383 xref: Reactome:268483 xref: Reactome:274226 xref: Reactome:274239 xref: Reactome:280695 xref: Reactome:282916 xref: Reactome:286582 xref: Reactome:286697 xref: Reactome:288391 xref: Reactome:289825 xref: Reactome:289866 xref: Reactome:290370 xref: Reactome:290403 xref: Reactome:291735 xref: Reactome:291787 xref: Reactome:292397 xref: Reactome:292434 xref: Reactome:293712 xref: Reactome:293765 xref: Reactome:73894 xref: Reactome:73942 is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0006308 name: DNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "DNA breakdown" EXACT [] synonym: "DNA catabolism" EXACT [] synonym: "DNA degradation" EXACT [] is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0006310 name: DNA recombination namespace: biological_process def: "The processes by which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0006325 name: establishment and/or maintenance of chromatin architecture namespace: biological_process def: "The specification, formation and maintenance of the physical structure of eukaryotic chromatin." [GOC:mah] subset: PANTHERGOslim is_a: GO:0006996 ! organelle organization and biogenesis [Term] id: GO:0006338 name: chromatin remodeling namespace: biological_process def: "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC:jic, PMID:12697820] subset: PANTHERGOslim synonym: "chromatin modeling" EXACT [] synonym: "chromatin modelling" EXACT [] synonym: "chromatin remodelling" EXACT [] is_a: GO:0006996 ! organelle organization and biogenesis [Term] id: GO:0006350 name: transcription namespace: biological_process def: "The synthesis of either RNA on a template of DNA or DNA on a template of RNA." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:212088 xref: Reactome:221846 xref: Reactome:230414 xref: Reactome:238456 xref: Reactome:244998 xref: Reactome:249880 xref: Reactome:252609 xref: Reactome:255785 xref: Reactome:259179 xref: Reactome:262535 xref: Reactome:265362 xref: Reactome:268499 xref: Reactome:274216 xref: Reactome:280685 xref: Reactome:282909 xref: Reactome:286705 xref: Reactome:288376 xref: Reactome:74159 is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0006357 name: regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators] subset: PANTHERGOslim synonym: "regulation of transcription from Pol II promoter" EXACT [] relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006366 name: transcription from RNA polymerase II promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase II (Pol II), originating at a Pol II-specific promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs)." [GOC:jl, ISBN:0321000382] subset: PANTHERGOslim synonym: "transcription from Pol II promoter" EXACT [] xref: Reactome:211919 xref: Reactome:221684 xref: Reactome:230271 xref: Reactome:238311 xref: Reactome:244872 xref: Reactome:249762 xref: Reactome:252544 xref: Reactome:255684 xref: Reactome:259080 xref: Reactome:262438 xref: Reactome:265275 xref: Reactome:268432 xref: Reactome:274112 xref: Reactome:280585 xref: Reactome:286603 xref: Reactome:288327 xref: Reactome:73857 is_a: GO:0006350 ! transcription [Term] id: GO:0006367 name: transcription initiation from RNA polymerase II promoter namespace: biological_process def: "Processes involved in starting transcription from the RNA polymerase II promoter." [GOC:jic] subset: PANTHERGOslim synonym: "transcription initiation from Pol II promoter" EXACT [] xref: Reactome:167161 xref: Reactome:211863 xref: Reactome:221628 xref: Reactome:230221 xref: Reactome:238260 xref: Reactome:244832 xref: Reactome:249731 xref: Reactome:255664 xref: Reactome:259054 xref: Reactome:262417 xref: Reactome:265256 xref: Reactome:274092 xref: Reactome:280567 xref: Reactome:286585 xref: Reactome:75953 relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006368 name: RNA elongation from RNA polymerase II promoter namespace: biological_process def: "The extension of an RNA molecule after transcription initiation at an RNA polymerase II-specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase II." [GOC:mah] subset: PANTHERGOslim synonym: "RNA elongation from Pol II promoter" EXACT [] xref: Reactome:167169 xref: Reactome:211622 xref: Reactome:221396 xref: Reactome:230030 xref: Reactome:238048 xref: Reactome:244663 xref: Reactome:249844 xref: Reactome:255756 xref: Reactome:259150 xref: Reactome:262507 xref: Reactome:265336 xref: Reactome:274185 xref: Reactome:280658 xref: Reactome:286677 xref: Reactome:288348 xref: Reactome:75955 relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006369 name: termination of RNA polymerase II transcription namespace: biological_process alt_id: GO:0019224 def: "The process by which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed." [GOC:mah] subset: PANTHERGOslim synonym: "RNA polymerase II transcription termination" EXACT [] synonym: "transcription termination from Pol II promoter" EXACT [] synonym: "transcription termination from RNA polymerase II promoter" EXACT [] xref: Reactome:167168 xref: Reactome:212031 xref: Reactome:221794 xref: Reactome:244958 xref: Reactome:286670 xref: Reactome:73856 relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0006370 name: mRNA capping namespace: biological_process def: "Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript." [GOC:mah, PMID:9266685] comment: See also the biological process term 'RNA capping ; GO:0009452'. subset: PANTHERGOslim synonym: "5' end capping" EXACT [] synonym: "5' mRNA capping" EXACT [] synonym: "5'-end mRNA processing" EXACT [] synonym: "5'-end processing" BROAD [] xref: Reactome:211717 xref: Reactome:221487 xref: Reactome:230111 xref: Reactome:238133 xref: Reactome:244728 xref: Reactome:249639 xref: Reactome:252428 xref: Reactome:255589 xref: Reactome:258966 xref: Reactome:262338 xref: Reactome:265186 xref: Reactome:274006 xref: Reactome:280485 xref: Reactome:286505 xref: Reactome:72086 is_a: GO:0006397 ! mRNA processing [Term] id: GO:0006378 name: mRNA polyadenylation namespace: biological_process def: "The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "cleavage and polyadenylylation specificity factor activity" NARROW [] synonym: "mRNA polyadenylylation" EXACT [] xref: Reactome:209549 xref: Reactome:219294 xref: Reactome:243459 xref: Reactome:248545 xref: Reactome:72185 is_a: GO:0031124 ! mRNA 3'-end processing [Term] id: GO:0006397 name: mRNA processing namespace: biological_process def: "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim synonym: "mRNA maturation" RELATED [] xref: Reactome:206758 xref: Reactome:212012 xref: Reactome:216307 xref: Reactome:221776 xref: Reactome:230353 xref: Reactome:241665 xref: Reactome:244946 xref: Reactome:249825 xref: Reactome:255781 xref: Reactome:259174 xref: Reactome:262531 xref: Reactome:265358 xref: Reactome:274212 xref: Reactome:284708 xref: Reactome:286661 xref: Reactome:75067 xref: Reactome:77586 is_a: GO:0016070 ! RNA metabolic process [Term] id: GO:0006399 name: tRNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "tRNA metabolism" EXACT [] is_a: GO:0016070 ! RNA metabolic process [Term] id: GO:0006401 name: RNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "RNA breakdown" EXACT [] synonym: "RNA catabolism" EXACT [] synonym: "RNA degradation" EXACT [] is_a: GO:0016070 ! RNA metabolic process [Term] id: GO:0006403 name: RNA localization namespace: biological_process def: "A process by which RNA is transported to, or maintained in, a specific location." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "establishment and maintenance of RNA localization" EXACT [] is_a: GO:0051179 ! localization [Term] id: GO:0006410 name: transcription, RNA-dependent namespace: biological_process def: "The synthesis of DNA on a template of RNA." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "reverse transcription" EXACT [] is_a: GO:0006350 ! transcription [Term] id: GO:0006412 name: translation namespace: biological_process alt_id: GO:0006416 alt_id: GO:0006453 alt_id: GO:0043037 def: "The chemical reactions and pathways resulting in the formation of a protein. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein formation" EXACT [] synonym: "protein synthesis" EXACT [] synonym: "protein translation" EXACT [] is_a: GO:0019538 ! protein metabolic process [Term] id: GO:0006417 name: regulation of translation namespace: biological_process alt_id: GO:0006445 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." [GOC:isa_complete] subset: gosubset_prok subset: PANTHERGOslim synonym: "regulation of protein anabolism" EXACT [] synonym: "regulation of protein biosynthesis" EXACT [] synonym: "regulation of protein formation" EXACT [] synonym: "regulation of protein synthesis" EXACT [] relationship: regulates GO:0006412 ! translation [Term] id: GO:0006418 name: tRNA aminoacylation for protein translation namespace: biological_process def: "The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis." [GOC:ma] subset: gosubset_prok subset: PANTHERGOslim synonym: "tRNA charging" NARROW [] xref: MetaCyc:TRNA-CHARGING-PWY relationship: part_of GO:0006412 ! translation [Term] id: GO:0006457 name: protein folding namespace: biological_process def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "chaperone activity" RELATED [] synonym: "chaperonin ATPase activity" RELATED [] synonym: "co-chaperone activity" RELATED [] synonym: "co-chaperonin activity" RELATED [] synonym: "glycoprotein-specific chaperone activity" RELATED [] synonym: "non-chaperonin molecular chaperone ATPase activity" RELATED [] synonym: "protein complex assembly, multichaperone pathway" RELATED [] is_a: GO:0019538 ! protein metabolic process [Term] id: GO:0006461 name: protein complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "chaperone activity" RELATED [] synonym: "protein complex biosynthesis" EXACT [] synonym: "protein complex formation" EXACT [] is_a: GO:0019538 ! protein metabolic process [Term] id: GO:0006464 name: protein modification process namespace: biological_process def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "process resulting in protein modification" RELATED [] synonym: "protein tagging activity" RELATED [] xref: Reactome:163841 xref: Reactome:212091 xref: Reactome:221849 xref: Reactome:230417 xref: Reactome:238459 xref: Reactome:245000 xref: Reactome:249885 xref: Reactome:252603 xref: Reactome:255790 xref: Reactome:259184 xref: Reactome:262540 xref: Reactome:268494 xref: Reactome:274221 xref: Reactome:280690 xref: Reactome:282898 xref: Reactome:286709 xref: Reactome:288370 is_a: GO:0019538 ! protein metabolic process [Term] id: GO:0006468 name: protein amino acid phosphorylation namespace: biological_process def: "The process of introducing a phosphate group on to a protein." [GOC:hb] subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:210076 xref: Reactome:219891 xref: Reactome:236701 xref: Reactome:73722 is_a: GO:0006464 ! protein modification process [Term] id: GO:0006471 name: protein amino acid ADP-ribosylation namespace: biological_process def: "The transfer, from NAD, of ADP-ribose to protein amino acids." [RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295] subset: gosubset_prok subset: PANTHERGOslim xref: RESID:AA0040 xref: RESID:AA0168 xref: RESID:AA0169 xref: RESID:AA0231 xref: RESID:AA0237 xref: RESID:AA0295 is_a: GO:0006464 ! protein modification process [Term] id: GO:0006473 name: protein amino acid acetylation namespace: biological_process def: "The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006464 ! protein modification process [Term] id: GO:0006479 name: protein amino acid methylation namespace: biological_process def: "The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006464 ! protein modification process [Term] id: GO:0006486 name: protein amino acid glycosylation namespace: biological_process def: "The addition of a sugar unit to a protein amino acid, e.g. the addition of glycan chains to proteins." [http://cancerweb.ncl.ac.uk/] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006464 ! protein modification process [Term] id: GO:0006497 name: protein amino acid lipidation namespace: biological_process alt_id: GO:0042050 def: "The covalent or non-covalent attachment of lipid moieties to an amino acid in a protein." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "lipid:protein modification" EXACT [] synonym: "protein lipidation" EXACT [] xref: RESID:AA0059 xref: RESID:AA0060 xref: RESID:AA0077 xref: RESID:AA0078 xref: RESID:AA0079 xref: RESID:AA0080 xref: RESID:AA0102 xref: RESID:AA0103 xref: RESID:AA0104 xref: RESID:AA0106 xref: RESID:AA0107 xref: RESID:AA0158 xref: RESID:AA0159 xref: RESID:AA0160 xref: RESID:AA0161 xref: RESID:AA0162 xref: RESID:AA0163 xref: RESID:AA0166 xref: RESID:AA0223 xref: RESID:AA0290 xref: RESID:AA0307 xref: RESID:AA0308 xref: RESID:AA0309 xref: RESID:AA0316 is_a: GO:0006464 ! protein modification process [Term] id: GO:0006508 name: proteolysis namespace: biological_process def: "The hydrolysis of a peptide bond or bonds within a protein." [GOC:jsg] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "peptidolysis" EXACT [] xref: Reactome:159782 xref: Reactome:211900 xref: Reactome:221664 xref: Reactome:230255 xref: Reactome:238291 is_a: GO:0019538 ! protein metabolic process [Term] id: GO:0006519 name: amino acid and derivative metabolic process namespace: biological_process def: "The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents, and compounds derived from amino acids." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "amino acid and derivative metabolism" EXACT [] is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0006520 name: amino acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "amino acid metabolism" EXACT [] is_a: GO:0006519 ! amino acid and derivative metabolic process [Term] id: GO:0006521 name: regulation of amino acid metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids." [GOC:go_curators] subset: gosubset_prok subset: PANTHERGOslim synonym: "regulation of amino acid metabolism" EXACT [] relationship: regulates GO:0006520 ! amino acid metabolic process [Term] id: GO:0006605 name: protein targeting namespace: biological_process def: "The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif." [GOC:ma] subset: gosubset_prok subset: PANTHERGOslim synonym: "nascent polypeptide association" RELATED [] is_a: GO:0006886 ! intracellular protein transport [Term] id: GO:0006629 name: lipid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "lipid metabolism" EXACT [] xref: Reactome:211949 xref: Reactome:221714 xref: Reactome:230304 xref: Reactome:238336 xref: Reactome:244894 xref: Reactome:249787 xref: Reactome:252529 xref: Reactome:255713 xref: Reactome:259099 xref: Reactome:262464 xref: Reactome:265294 xref: Reactome:268417 xref: Reactome:274140 xref: Reactome:280613 xref: Reactome:282852 xref: Reactome:286671 xref: Reactome:288319 xref: Reactome:289875 xref: Reactome:290413 xref: Reactome:291758 xref: Reactome:292446 xref: Reactome:293732 xref: Reactome:73923 is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0006631 name: fatty acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim synonym: "fatty acid metabolism" EXACT [] xref: Reactome:207636 xref: Reactome:217132 xref: Reactome:242340 xref: Reactome:247601 xref: Reactome:267118 xref: Reactome:272214 xref: Reactome:278210 xref: Reactome:76466 is_a: GO:0006629 ! lipid metabolic process [Term] id: GO:0006633 name: fatty acid biosynthetic process namespace: biological_process alt_id: GO:0000037 def: "The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "fatty acid anabolism" EXACT [] synonym: "fatty acid biosynthesis" EXACT [] synonym: "fatty acid formation" EXACT [] synonym: "fatty acid synthesis" EXACT [] xref: MetaCyc:FASYN-INITIAL-PWY xref: MetaCyc:PWY-4381 xref: MetaCyc:PWY-5156 is_a: GO:0006631 ! fatty acid metabolic process [Term] id: GO:0006635 name: fatty acid beta-oxidation namespace: biological_process def: "The metabolic oxidation of a long-chain fatty acid by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:109339 xref: Reactome:109341 xref: Reactome:109342 xref: Reactome:109343 xref: Reactome:109998 xref: Reactome:207162 xref: Reactome:209200 xref: Reactome:210740 xref: Reactome:210841 xref: Reactome:210856 xref: Reactome:211757 xref: Reactome:212036 xref: Reactome:216731 xref: Reactome:218933 xref: Reactome:220631 xref: Reactome:220691 xref: Reactome:220706 xref: Reactome:221524 xref: Reactome:221800 xref: Reactome:227736 xref: Reactome:229307 xref: Reactome:229381 xref: Reactome:229389 xref: Reactome:230202 xref: Reactome:230396 xref: Reactome:234264 xref: Reactome:235965 xref: Reactome:237300 xref: Reactome:237395 xref: Reactome:237408 xref: Reactome:238167 xref: Reactome:238413 xref: Reactome:242015 xref: Reactome:243139 xref: Reactome:244757 xref: Reactome:244960 xref: Reactome:247389 xref: Reactome:249130 xref: Reactome:249663 xref: Reactome:249839 xref: Reactome:251206 xref: Reactome:252064 xref: Reactome:252445 xref: Reactome:252572 xref: Reactome:255267 xref: Reactome:255679 xref: Reactome:255782 xref: Reactome:258563 xref: Reactome:259074 xref: Reactome:259175 xref: Reactome:265366 xref: Reactome:267507 xref: Reactome:267955 xref: Reactome:268368 xref: Reactome:268473 xref: Reactome:273504 xref: Reactome:274108 xref: Reactome:274213 xref: Reactome:279976 xref: Reactome:280581 xref: Reactome:280682 xref: Reactome:286710 xref: Reactome:289872 xref: Reactome:291790 xref: Reactome:293500 xref: Reactome:293508 xref: Reactome:293509 xref: Reactome:293718 xref: Reactome:293767 xref: Reactome:77288 xref: Reactome:77289 is_a: GO:0006631 ! fatty acid metabolic process [Term] id: GO:0006636 name: unsaturated fatty acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an unsaturated fatty acid, any fatty acid containing one or more double bonds between carbon atoms." [GOC:mah, MetaCyc:PWY-762, MetaCyc:PWY-782] subset: gosubset_prok subset: PANTHERGOslim synonym: "fatty acid desaturation" RELATED [] synonym: "unsaturated fatty acid anabolism" EXACT [] synonym: "unsaturated fatty acid biosynthesis" EXACT [] synonym: "unsaturated fatty acid formation" EXACT [] synonym: "unsaturated fatty acid synthesis" EXACT [] xref: MetaCyc:PWY-762 xref: MetaCyc:PWY-782 is_a: GO:0006633 ! fatty acid biosynthetic process [Term] id: GO:0006637 name: acyl-CoA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty-acyl group." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "acyl-CoA metabolism" EXACT [] is_a: GO:0006631 ! fatty acid metabolic process is_a: GO:0006732 ! coenzyme metabolic process [Term] id: GO:0006644 name: phospholipid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "phospholipid metabolism" EXACT [] is_a: GO:0006629 ! lipid metabolic process [Term] id: GO:0006732 name: coenzyme metabolic process namespace: biological_process def: "The chemical reactions and pathways involving coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "coenzyme and prosthetic group metabolic process" BROAD [] synonym: "coenzyme and prosthetic group metabolism" BROAD [] synonym: "coenzyme metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006766 name: vitamin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems." [GOC:ai] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "vitamin metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006778 name: porphyrin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving any member of a large group of derivatives or analogs of porphyrin. Porphyrins consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "porphyrin metabolism" EXACT [] xref: Reactome:189445 xref: Reactome:211983 xref: Reactome:221747 xref: Reactome:230328 xref: Reactome:238365 xref: Reactome:244922 xref: Reactome:249883 xref: Reactome:252549 xref: Reactome:255726 xref: Reactome:259119 xref: Reactome:262477 xref: Reactome:265308 xref: Reactome:268438 xref: Reactome:274151 xref: Reactome:280624 xref: Reactome:286643 xref: Reactome:288330 xref: Reactome:289847 xref: Reactome:290388 xref: Reactome:291767 xref: Reactome:292417 xref: Reactome:293743 is_a: GO:0008152 ! metabolic process [Term] id: GO:0006790 name: sulfur metabolic process namespace: biological_process def: "The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "sulfur metabolism" EXACT [] synonym: "sulphur metabolic process" EXACT [] synonym: "sulphur metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006796 name: phosphate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "phosphate metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006798 name: polyphosphate catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of a polyphosphate, the anion or salt of polyphosphoric acid." [GOC:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "polyphosphate breakdown" EXACT [] synonym: "polyphosphate catabolism" EXACT [] synonym: "polyphosphate degradation" EXACT [] is_a: GO:0006796 ! phosphate metabolic process [Term] id: GO:0006800 name: oxygen and reactive oxygen species metabolic process namespace: biological_process def: "The chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH)." [GOC:jl, PMID:12115731] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "oxygen and active oxygen species metabolism" EXACT [] synonym: "oxygen and AOS metabolism" EXACT [] synonym: "oxygen and reactive oxidative species metabolism" EXACT [] synonym: "oxygen and reactive oxygen intermediate metabolism" EXACT [] synonym: "oxygen and reactive oxygen species metabolism" EXACT [] synonym: "oxygen and ROI metabolism" EXACT [] synonym: "oxygen and ROS metabolic process" EXACT [] synonym: "oxygen and ROS metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006807 name: nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds; includes nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium." [GOC:go_curators, GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node. subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "nitrogen compound metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006809 name: nitric oxide biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "nitric oxide anabolism" EXACT [] synonym: "nitric oxide biosynthesis" EXACT [] synonym: "nitric oxide formation" EXACT [] synonym: "nitric oxide synthesis" EXACT [] is_a: GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0006810 name: transport namespace: biological_process def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells." [GOC:mah] comment: Note that 'electron transport ; GO:0006118' is not a child of transport because electron transport is not a type of directed movement of substances. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "small molecule transport" NARROW [] synonym: "solute:solute exchange" NARROW [] is_a: GO:0008150 ! biological_process [Term] id: GO:0006811 name: ion transport namespace: biological_process def: "The directed movement of charged atoms or small charged molecules into, out of, within or between cells." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0006812 name: cation transport namespace: biological_process alt_id: GO:0006819 def: "The directed movement of cations, atoms or small molecules with a net positive charge, into, out of, within or between cells." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006811 ! ion transport [Term] id: GO:0006817 name: phosphate transport namespace: biological_process def: "The directed movement of phosphate into, out of, within or between cells." [GOC:krc] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0006820 name: anion transport namespace: biological_process alt_id: GO:0006822 def: "The directed movement of anions, atoms or small molecules with a net negative charge, into, out of, within or between cells." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006811 ! ion transport [Term] id: GO:0006839 name: mitochondrial transport namespace: biological_process def: "Transport of substances into, out of or within a mitochondrion." [GOC:ai] subset: PANTHERGOslim synonym: "mitochondrial alpha-ketoglutarate/malate transport" NARROW [] synonym: "mitochondrial aspartate/glutamate transport" NARROW [] synonym: "mitochondrial sodium/calcium ion exchange" NARROW [] relationship: part_of GO:0007005 ! mitochondrion organization and biogenesis [Term] id: GO:0006858 name: extracellular transport namespace: biological_process def: "The transport of substances that occurs outside cells." [GOC:go_curators] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0006865 name: amino acid transport namespace: biological_process alt_id: GO:0006866 def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0006869 name: lipid transport namespace: biological_process def: "The directed movement of lipids into, out of, within or between cells. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0006874 name: cellular calcium ion homeostasis namespace: biological_process def: "The regulation of the levels, transport, and metabolism of calcium ions within a cell or between a cell and its external environment." [GOC:ceb] subset: PANTHERGOslim synonym: "regulation of calcium ion concentration" BROAD [] is_a: GO:0042592 ! homeostatic process [Term] id: GO:0006886 name: intracellular protein transport namespace: biological_process def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0015031 ! protein transport [Term] id: GO:0006887 name: exocytosis namespace: biological_process alt_id: GO:0016194 alt_id: GO:0016195 def: "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell. This is the process whereby most molecules are secreted from eukaryotic cells." [ISBN:0716731363] subset: gosubset_prok subset: PANTHERGOslim synonym: "nonselective vesicle exocytosis" RELATED [] synonym: "vesicle exocytosis" EXACT [] is_a: GO:0016192 ! vesicle-mediated transport [Term] id: GO:0006897 name: endocytosis namespace: biological_process alt_id: GO:0016193 alt_id: GO:0016196 def: "The uptake of external materials by cells by the invagination of small region of the plasma membrane to form a new intracellular membrane-limited vesicle." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology", ISBN:0716731363] subset: gosubset_prok subset: PANTHERGOslim synonym: "nonselective vesicle endocytosis" RELATED [] synonym: "plasma membrane invagination" EXACT [] synonym: "vesicle endocytosis" EXACT [] is_a: GO:0016192 ! vesicle-mediated transport [Term] id: GO:0006898 name: receptor-mediated endocytosis namespace: biological_process def: "The uptake of external materials by cells, utilizing receptors to ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles." [ISBN:0716731363] subset: PANTHERGOslim synonym: "receptor mediated endocytosis" EXACT [] xref: Reactome:171052 xref: Reactome:171059 xref: Reactome:171087 xref: Reactome:171106 xref: Reactome:171118 xref: Reactome:171122 xref: Reactome:171141 xref: Reactome:174624 xref: Reactome:174657 xref: Reactome:174808 xref: Reactome:206358 xref: Reactome:206384 xref: Reactome:206399 xref: Reactome:209279 xref: Reactome:209288 xref: Reactome:209290 xref: Reactome:209306 xref: Reactome:209307 xref: Reactome:211842 xref: Reactome:215912 xref: Reactome:215938 xref: Reactome:215954 xref: Reactome:219043 xref: Reactome:219049 xref: Reactome:219051 xref: Reactome:219061 xref: Reactome:219062 xref: Reactome:221607 xref: Reactome:227815 xref: Reactome:227829 xref: Reactome:227832 xref: Reactome:227846 xref: Reactome:227847 xref: Reactome:230205 xref: Reactome:233525 xref: Reactome:233547 xref: Reactome:233560 xref: Reactome:236045 xref: Reactome:236052 xref: Reactome:236054 xref: Reactome:236066 xref: Reactome:236067 xref: Reactome:238242 xref: Reactome:243198 xref: Reactome:243209 xref: Reactome:243215 xref: Reactome:243225 xref: Reactome:243226 xref: Reactome:244815 xref: Reactome:248328 xref: Reactome:249712 is_a: GO:0006897 ! endocytosis [Term] id: GO:0006907 name: pinocytosis namespace: biological_process def: "The process whereby cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "fluid-phase endocytosis" EXACT [] is_a: GO:0006897 ! endocytosis [Term] id: GO:0006909 name: phagocytosis namespace: biological_process def: "The process whereby phagocytes engulf external particulate material. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim is_a: GO:0006897 ! endocytosis [Term] id: GO:0006915 name: apoptosis namespace: biological_process def: "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle the cell and result in cell death. Apoptosis begins internally with condensation and subsequent fragmentation of the cell nucleus (blebbing) while the plasma membrane remains intact. Other characteristics of apoptosis include DNA fragmentation and the exposure of phosphatidyl serine on the cell surface." [GOC:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "apoptotic programmed cell death" EXACT [] synonym: "programmed cell death by apoptosis" EXACT [] synonym: "signaling (initiator) caspase activity" RELATED [] synonym: "type I programmed cell death" NARROW [] xref: Reactome:109581 xref: Reactome:212025 xref: Reactome:221788 xref: Reactome:230365 xref: Reactome:238478 xref: Reactome:245020 xref: Reactome:249908 xref: Reactome:252627 xref: Reactome:255810 xref: Reactome:259206 xref: Reactome:262565 xref: Reactome:265386 xref: Reactome:268517 xref: Reactome:274243 xref: Reactome:280709 xref: Reactome:286733 xref: Reactome:288390 is_a: GO:0008150 ! biological_process [Term] id: GO:0006917 name: induction of apoptosis namespace: biological_process def: "A process that directly activates any of the steps required for cell death by apoptosis." [GOC:go_curators] subset: PANTHERGOslim synonym: "activation of apoptosis" EXACT [] synonym: "apoptosis activator activity" RELATED [] synonym: "apoptosis signaling" BROAD [] synonym: "commitment to apoptosis" EXACT [] synonym: "induction of apoptosis by p53" NARROW [] is_a: GO:0006915 ! apoptosis [Term] id: GO:0006928 name: cell motility namespace: biological_process def: "Any process involved in the controlled movement of a cell." [GOC:jl] subset: goslim_goa subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "cell locomotion" EXACT [] synonym: "cell movement" EXACT [] is_a: GO:0009987 ! cellular process [Term] id: GO:0006936 name: muscle contraction namespace: biological_process def: "A process whereby force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step. The chemo-mechanical energy conversion step is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis." [GOC:ef, GOC:mtg_muscle, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_pir subset: PANTHERGOslim is_a: GO:0003008 ! system process [Term] id: GO:0006950 name: response to stress namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0050896 ! response to stimulus [Term] id: GO:0006955 name: immune response namespace: biological_process def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [GOC:add, GOC:mtg_15nov05] comment: This term was improved by GO_REF:0000022. It was redefined and moved. subset: PANTHERGOslim is_a: GO:0002376 ! immune system process is_a: GO:0050896 ! response to stimulus [Term] id: GO:0006956 name: complement activation namespace: biological_process def: "Processes involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway." [GOC:add, GOC:mtg_15nov05, ISBN:0781735149 "Fundamental Immunology"] comment: This term was improved by GO_REF:0000022. It was moved. subset: PANTHERGOslim synonym: "complement activity" RELATED [] synonym: "complement response" EXACT [] xref: Reactome:166663 xref: Reactome:211734 xref: Reactome:221852 xref: Reactome:230422 is_a: GO:0006955 ! immune response [Term] id: GO:0006968 name: cellular defense response namespace: biological_process alt_id: GO:0016066 alt_id: GO:0016067 def: "A defense response that is mediated by cells." [GOC:ebc] comment: Note that this term refers to any type of defense response made by any cell, whether only a single-celled organism or part of a multicellular organism. subset: PANTHERGOslim synonym: "cellular defence response" EXACT [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0006996 name: organelle organization and biogenesis namespace: biological_process def: "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of any organelle within a cell." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "organelle organisation and biogenesis" EXACT [] is_a: GO:0016043 ! cellular component organization and biogenesis [Term] id: GO:0007005 name: mitochondrion organization and biogenesis namespace: biological_process def: "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphology and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components." [GOC:mah, GOC:sgd_curators, PMID:9786946] subset: goslim_generic subset: goslim_pir subset: PANTHERGOslim synonym: "mitochondria organization and biogenesis" EXACT [] synonym: "mitochondrion organisation and biogenesis" EXACT [] is_a: GO:0006996 ! organelle organization and biogenesis [Term] id: GO:0007010 name: cytoskeleton organization and biogenesis namespace: biological_process def: "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "cytoskeletal organization and biogenesis" EXACT [] synonym: "cytoskeletal regulator activity" RELATED [] synonym: "cytoskeleton organisation and biogenesis" EXACT [] is_a: GO:0006996 ! organelle organization and biogenesis [Term] id: GO:0007028 name: cytoplasm organization and biogenesis namespace: biological_process def: "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of the cytoplasm and its components." [GOC:curators] subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "cytoplasm organisation and biogenesis" EXACT [] is_a: GO:0016043 ! cellular component organization and biogenesis [Term] id: GO:0007041 name: lysosomal transport namespace: biological_process def: "The directed movement of substances into, out of or within a lysosome." [GOC:ai] subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0007049 name: cell cycle namespace: biological_process def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "cell-division cycle" EXACT [] is_a: GO:0008150 ! biological_process is_a: GO:0009987 ! cellular process [Term] id: GO:0007059 name: chromosome segregation namespace: biological_process def: "The process by which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets." [GOC:ai] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "chromosome division" EXACT [] synonym: "chromosome transmission" RELATED [] is_a: GO:0009987 ! cellular process [Term] id: GO:0007067 name: mitosis namespace: biological_process def: "Progression through mitosis, the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother." [GOC:ma, ISBN:0198547684] subset: PANTHERGOslim is_a: GO:0007049 ! cell cycle [Term] id: GO:0007126 name: meiosis namespace: biological_process def: "Progression through meiosis, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiosis occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations." [PMID:9334324] subset: goslim_yeast subset: PANTHERGOslim is_a: GO:0007049 ! cell cycle [Term] id: GO:0007154 name: cell communication namespace: biological_process def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0008150 ! biological_process is_a: GO:0009987 ! cellular process [Term] id: GO:0007155 name: cell adhesion namespace: biological_process def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf] subset: goslim_candida subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "cell adhesion molecule activity" RELATED [] is_a: GO:0008150 ! biological_process is_a: GO:0009987 ! cellular process [Term] id: GO:0007160 name: cell-matrix adhesion namespace: biological_process def: "The binding of a cell to the extracellular matrix via adhesion molecules." [GOC:hb] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0007155 ! cell adhesion [Term] id: GO:0007165 name: signal transduction namespace: biological_process def: "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell." [GOC:go_curators] subset: goslim_candida subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "signaling" EXACT [] synonym: "signaling cascade" EXACT [] synonym: "signalling" EXACT [] synonym: "signalling cascade" EXACT [] is_a: GO:0007154 ! cell communication [Term] id: GO:0007166 name: cell surface receptor linked signal transduction namespace: biological_process def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:110437 is_a: GO:0007165 ! signal transduction [Term] id: GO:0007169 name: transmembrane receptor protein tyrosine kinase signaling pathway namespace: biological_process def: "The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand." [GOC:ceb] subset: PANTHERGOslim synonym: "transmembrane receptor protein tyrosine kinase signalling pathway" EXACT [] is_a: GO:0007166 ! cell surface receptor linked signal transduction [Term] id: GO:0007178 name: transmembrane receptor protein serine/threonine kinase signaling pathway namespace: biological_process def: "The series of molecular signals generated as a consequence of a transmembrane receptor serine/threonine kinase binding to its physiological ligand." [GOC:mah] subset: PANTHERGOslim synonym: "transmembrane receptor protein serine/threonine kinase signalling pathway" EXACT [] is_a: GO:0007166 ! cell surface receptor linked signal transduction [Term] id: GO:0007186 name: G-protein coupled receptor protein signaling pathway namespace: biological_process def: "The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand." [GOC:mah] subset: PANTHERGOslim synonym: "G protein coupled receptor protein signaling pathway" EXACT [] synonym: "G protein coupled receptor protein signalling pathway" EXACT [] synonym: "G-protein coupled receptor protein signalling pathway" EXACT [] synonym: "G-protein-coupled receptor protein signaling pathway" EXACT [] synonym: "G-protein-coupled receptor protein signalling pathway" EXACT [] synonym: "GPCR protein signaling pathway" EXACT [] synonym: "GPCR protein signalling pathway" EXACT [] is_a: GO:0007166 ! cell surface receptor linked signal transduction [Term] id: GO:0007242 name: intracellular signaling cascade namespace: biological_process def: "A series of reactions within the cell that occur as a result of a single trigger reaction or compound." [GOC:jl, http://cancerweb.ncl.ac.uk/] subset: gosubset_prok subset: PANTHERGOslim synonym: "intracellular signalling cascade" EXACT [] is_a: GO:0007165 ! signal transduction [Term] id: GO:0007249 name: I-kappaB kinase/NF-kappaB cascade namespace: biological_process def: "A series of reactions initiated by the activation of the transcription factor NF-kappaB. NF-kappaB is sequestered by the inhibitor I-kappaB, and is released when I-kappaB is phosphorylated by activated I-kappaB kinase." [GOC:jl, PMID:12773372] subset: PANTHERGOslim synonym: "activation of the inhibitor of kappa kinase" RELATED [] synonym: "NIK-I-kappaB/NF-kappaB cascade" EXACT [] xref: Reactome:166058 xref: Reactome:166166 xref: Reactome:211840 xref: Reactome:238238 is_a: GO:0007242 ! intracellular signaling cascade [Term] id: GO:0007254 name: JNK cascade namespace: biological_process def: "A cascade of protein kinase activities, culminating in the phosphorylation and activation of a member of the JUN kinase subfamily of stress-activated protein kinases, which in turn are a subfamily of mitogen-activated protein (MAP) kinases that is activated primarily by cytokines and exposure to environmental stress." [GOC:bf, PMID:11790549] subset: PANTHERGOslim synonym: "SAPK cascade" BROAD [] synonym: "stress-activated protein kinase cascade" BROAD [] is_a: GO:0000165 ! MAPKKK cascade [Term] id: GO:0007259 name: JAK-STAT cascade namespace: biological_process def: "The processes by which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of cytokines to their cognate receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes." [GOC:jl, PMID:12039028] subset: PANTHERGOslim is_a: GO:0007242 ! intracellular signaling cascade [Term] id: GO:0007263 name: nitric oxide mediated signal transduction namespace: biological_process def: "A series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:jl] subset: PANTHERGOslim synonym: "nitric oxide-mediated signal transduction" EXACT [] synonym: "NO mediated signal transduction" EXACT [] synonym: "NO-mediated signal transduction" EXACT [] is_a: GO:0007242 ! intracellular signaling cascade [Term] id: GO:0007267 name: cell-cell signaling namespace: biological_process def: "Any process that mediates the transfer of information from one cell to another." [GOC:mah] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "cell-cell signalling" EXACT [] is_a: GO:0007154 ! cell communication [Term] id: GO:0007268 name: synaptic transmission namespace: biological_process def: "The process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse." [GOC:jl, MeSH:D009435] subset: PANTHERGOslim synonym: "neurotransmission" RELATED [GOC:dph] synonym: "regulation of synapse" RELATED [] is_a: GO:0007267 ! cell-cell signaling [Term] id: GO:0007269 name: neurotransmitter secretion namespace: biological_process def: "The regulated release of neurotransmitter into the synaptic cleft. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, y aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin." [GOC:dph, http://cancerweb.ncl.ac.uk] subset: PANTHERGOslim synonym: "neurotransmitter release" EXACT [] is_a: GO:0050877 ! neurological system process [Term] id: GO:0007270 name: nerve-nerve synaptic transmission namespace: biological_process def: "The process of communication from a neuron to another neuron across a synapse." [GOC:jl, MeSH:D009435] subset: PANTHERGOslim is_a: GO:0007268 ! synaptic transmission [Term] id: GO:0007274 name: neuromuscular synaptic transmission namespace: biological_process def: "The process of communication from a neuron to a muscle, across a synapse." [GOC:jl, MeSH:D009435] subset: PANTHERGOslim is_a: GO:0007268 ! synaptic transmission [Term] id: GO:0007276 name: gamete generation namespace: biological_process alt_id: GO:0009552 def: "The generation and maintenance of gametes. A gamete is a haploid reproductive cell." [GOC:ems, GOC:mtg_sensu] subset: PANTHERGOslim synonym: "gamete generation (sensu Magnoliophyta)" RELATED [] synonym: "gametogenesis" RELATED [] is_a: GO:0000003 ! reproduction [Term] id: GO:0007283 name: spermatogenesis namespace: biological_process def: "The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis." [GOC:jic, http://cancerweb.ncl.ac.uk] subset: PANTHERGOslim synonym: "generation of spermatozoa" EXACT [] is_a: GO:0007276 ! gamete generation [Term] id: GO:0007292 name: female gamete generation namespace: biological_process def: "Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction." [GOC:dph, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim is_a: GO:0007276 ! gamete generation [Term] id: GO:0007379 name: segment specification namespace: biological_process def: "The process whereby segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238] subset: PANTHERGOslim is_a: GO:0007389 ! pattern specification process [Term] id: GO:0007389 name: pattern specification process namespace: biological_process def: "The developmental processes that result in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." [GOC:go_curators, GOC:isa_complete, ISBN:0521436125] subset: PANTHERGOslim synonym: "pattern biosynthesis" RELATED [] synonym: "pattern formation" RELATED [] is_a: GO:0032502 ! developmental process [Term] id: GO:0007398 name: ectoderm development namespace: biological_process def: "The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation." [GOC:dph, GOC:tb] subset: PANTHERGOslim is_a: GO:0032502 ! developmental process [Term] id: GO:0007399 name: nervous system development namespace: biological_process def: "The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state." [GOC:dgh] subset: PANTHERGOslim synonym: "neurite biosynthesis" EXACT [] synonym: "neurite formation" EXACT [] synonym: "neurite growth" EXACT [] synonym: "pan-neural process" RELATED [] is_a: GO:0048731 ! system development [Term] id: GO:0007492 name: endoderm development namespace: biological_process def: "The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues." [GOC:dph, GOC:tb] subset: PANTHERGOslim is_a: GO:0032502 ! developmental process [Term] id: GO:0007498 name: mesoderm development namespace: biological_process def: "The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue." [GOC:dph, GOC:tb] subset: PANTHERGOslim is_a: GO:0032502 ! developmental process [Term] id: GO:0007502 name: gut mesoderm development namespace: biological_process def: "The process whose specific outcome is the progression of the gut mesoderm over time, from its formation to the mature structure. The gut mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gut of the organism." [GOC:ai] subset: PANTHERGOslim is_a: GO:0007498 ! mesoderm development [Term] id: GO:0007507 name: heart development namespace: biological_process alt_id: GO:0007511 def: "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." [GOC:jic, http://cancerweb.ncl.ac.uk] subset: PANTHERGOslim synonym: "cardiac development" RELATED [] synonym: "dorsal vessel development" NARROW [] is_a: GO:0048731 ! system development [Term] id: GO:0007517 name: muscle development namespace: biological_process def: "The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work." [GOC:jic, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim is_a: GO:0048731 ! system development [Term] id: GO:0007530 name: sex determination namespace: biological_process def: "Any process that establishes and transmits the specification of sexual status of an individual organism." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim is_a: GO:0032502 ! developmental process [Term] id: GO:0007596 name: blood coagulation namespace: biological_process def: "The sequential process by which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers." [http://www.graylab.ac.uk/omd/, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "blood clotting" EXACT [] xref: Reactome:140875 xref: Reactome:140877 xref: Reactome:211647 xref: Reactome:211988 xref: Reactome:221419 xref: Reactome:221752 xref: Reactome:230054 xref: Reactome:230334 xref: Reactome:238072 xref: Reactome:238370 xref: Reactome:244684 xref: Reactome:244925 is_a: GO:0009605 ! response to external stimulus [Term] id: GO:0007600 name: sensory perception namespace: biological_process def: "The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal." [GOC:ai, GOC:dph] subset: PANTHERGOslim is_a: GO:0050877 ! neurological system process [Term] id: GO:0007601 name: visual perception namespace: biological_process def: "The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image." [GOC:ai] subset: PANTHERGOslim synonym: "sense of sight" EXACT [] synonym: "sensory visual perception" EXACT [] synonym: "vision" EXACT [] is_a: GO:0003008 ! system process [Term] id: GO:0007605 name: sensory perception of sound namespace: biological_process def: "The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound." [GOC:ai] subset: PANTHERGOslim synonym: "hearing" EXACT [] synonym: "perception of sound" EXACT [] is_a: GO:0003008 ! system process [Term] id: GO:0007606 name: sensory perception of chemical stimulus namespace: biological_process def: "The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal." [GOC:ai] subset: PANTHERGOslim synonym: "chemosensory perception" EXACT [] is_a: GO:0007600 ! sensory perception [Term] id: GO:0007608 name: sensory perception of smell namespace: biological_process def: "The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors." [GOC:ai, http://www.onelook.com/] subset: PANTHERGOslim synonym: "olfaction" EXACT [] synonym: "scent perception" EXACT [] synonym: "sense of smell" EXACT [] synonym: "smell perception" EXACT [] is_a: GO:0007606 ! sensory perception of chemical stimulus [Term] id: GO:0007610 name: behavior namespace: biological_process def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [GOC:ems, ISBN:0395448956] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "behavioral response to stimulus" EXACT [] synonym: "behaviour" EXACT [] synonym: "behavioural response to stimulus" EXACT [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0008009 name: chemokine activity namespace: molecular_function def: "The function of a family of chemotactic pro-inflammatory activation-inducible cytokines acting primarily upon hemopoietic cells in immunoregulatory processes; all chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation." [http://www.copewithcytokines.de/cope.cgi?001252] comment: See also the molecular function term 'cytokine activity ; GO:0005125'. subset: PANTHERGOslim is_a: GO:0005125 ! cytokine activity [Term] id: GO:0008015 name: blood circulation namespace: biological_process def: "The flow of blood through the body of an animal, enabling the transport of O2 and nutrients to the tissues and the removal of waste products." [ISBN:0192800825] subset: goslim_pir subset: PANTHERGOslim is_a: GO:0003008 ! system process [Term] id: GO:0008017 name: microtubule binding namespace: molecular_function def: "Interacting selectively with microtubules, filaments composed of tubulin monomers." [GOC:krc] subset: PANTHERGOslim synonym: "microtubule severing activity" RELATED [] synonym: "microtubule/chromatin interaction" RELATED [] is_a: GO:0008092 ! cytoskeletal protein binding [Term] id: GO:0008037 name: cell recognition namespace: biological_process def: "The process by which a cell in a multicellular organism interprets its surroundings." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: PANTHERGOslim is_a: GO:0009987 ! cellular process [Term] id: GO:0008047 name: enzyme activator activity namespace: molecular_function def: "Increases the activity of an enzyme." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0030234 ! enzyme regulator activity [Term] id: GO:0008066 name: glutamate receptor activity namespace: molecular_function def: "Combining with glutamate to initiate a change in cell activity." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0004872 ! receptor activity [Term] id: GO:0008081 name: phosphoric diester hydrolase activity namespace: molecular_function alt_id: GO:0016792 def: "Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group." [http://cancerweb.ncl.ac.uk/] subset: gosubset_prok subset: PANTHERGOslim synonym: "endonuclease VIII activity" RELATED [] synonym: "phosphodiesterase" NARROW [] xref: EC:3.1.4 is_a: GO:0016788 ! hydrolase activity, acting on ester bonds [Term] id: GO:0008083 name: growth factor activity namespace: molecular_function def: "The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation." [ISBN:0815316194] subset: PANTHERGOslim is_a: GO:0005102 ! receptor binding [Term] id: GO:0008092 name: cytoskeletal protein binding namespace: molecular_function def: "Interacting selectively with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah] subset: goslim_generic subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005515 ! protein binding [Term] id: GO:0008104 name: protein localization namespace: biological_process def: "The processes by which a protein is transported to, or maintained in, a specific location." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "establishment and maintenance of protein localization" EXACT [] is_a: GO:0051179 ! localization [Term] id: GO:0008105 name: asymmetric protein localization namespace: biological_process def: "The processes by which a protein is transported to, or maintained in, a specific asymmetric distribution." [GOC:ma] subset: gosubset_prok subset: PANTHERGOslim synonym: "establishment and maintenance of asymmetric protein localization" EXACT [] is_a: GO:0008104 ! protein localization [Term] id: GO:0008135 name: translation factor activity, nucleic acid binding namespace: molecular_function def: "Functions during translation by binding nucleic acids during polypeptide synthesis at the ribosome." [GOC:ai] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003676 ! nucleic acid binding [Term] id: GO:0008143 name: poly(A) binding namespace: molecular_function def: "Interacting selectively with the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "poly-A binding" EXACT [] synonym: "polyadenylate binding" EXACT [] is_a: GO:0003729 ! mRNA binding [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 def: "Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "biological process unknown" NARROW [] synonym: "physiological process" EXACT [] [Term] id: GO:0008152 name: metabolic process namespace: biological_process def: "Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" NARROW [] xref: Reactome:212093 xref: Reactome:221851 xref: Reactome:230419 xref: Reactome:238461 xref: Reactome:245002 xref: Reactome:249887 xref: Reactome:252604 xref: Reactome:255791 xref: Reactome:259186 xref: Reactome:262542 xref: Reactome:265367 xref: Reactome:268496 xref: Reactome:274223 xref: Reactome:280692 xref: Reactome:282903 xref: Reactome:286711 xref: Reactome:288374 xref: Reactome:289882 xref: Reactome:290414 xref: Reactome:291791 xref: Reactome:292439 xref: Reactome:293772 xref: Reactome:71408 is_a: GO:0008150 ! biological_process [Term] id: GO:0008168 name: methyltransferase activity namespace: molecular_function alt_id: GO:0004480 def: "Catalysis of the transfer of a methyl group to an acceptor molecule." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "methylase" BROAD [] xref: EC:2.1.1 xref: Reactome:1062 is_a: GO:0016740 ! transferase activity [Term] id: GO:0008173 name: RNA methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule." [GOC:mah] comment: Note that the methyl donor is usually S-adenosyl-L-methionine, but there is at least one exception (see GO:0030698). subset: gosubset_prok subset: PANTHERGOslim xref: EC:2.1.1.- is_a: GO:0008168 ! methyltransferase activity [Term] id: GO:0008191 name: metalloendopeptidase inhibitor activity namespace: molecular_function def: "Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides and contain a chelated metal ion at their active sites which is essential to their catalytic activity." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "metalloprotease inhibitor" BROAD [] synonym: "metalloproteinase inhibitor" BROAD [] is_a: GO:0030414 ! protease inhibitor activity [Term] id: GO:0008202 name: steroid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [ISBN:0198547684] subset: gosubset_prok subset: PANTHERGOslim synonym: "steroid metabolism" EXACT [] xref: Reactome:192076 xref: Reactome:211979 xref: Reactome:221744 xref: Reactome:230324 xref: Reactome:238361 xref: Reactome:244919 xref: Reactome:249836 xref: Reactome:252547 xref: Reactome:255724 xref: Reactome:259117 xref: Reactome:262501 xref: Reactome:265331 xref: Reactome:268436 xref: Reactome:274179 xref: Reactome:280652 xref: Reactome:286641 xref: Reactome:289845 xref: Reactome:290393 xref: Reactome:291785 xref: Reactome:293762 is_a: GO:0006629 ! lipid metabolic process [Term] id: GO:0008203 name: cholesterol metabolic process namespace: biological_process def: "The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "cholesterol metabolism" EXACT [] is_a: GO:0008202 ! steroid metabolic process [Term] id: GO:0008206 name: bile acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [GOC:go_curators] subset: PANTHERGOslim synonym: "bile acid metabolism" EXACT [] is_a: GO:0008202 ! steroid metabolic process [Term] id: GO:0008219 name: cell death namespace: biological_process def: "The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:ems] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "necrosis" RELATED [] is_a: GO:0016265 ! death [Term] id: GO:0008233 name: peptidase activity namespace: molecular_function def: "Catalysis of the hydrolysis of peptide bonds." [GOC:jl] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "hydrolase, acting on peptide bonds" EXACT [] synonym: "peptide hydrolase activity" EXACT [] synonym: "protease activity" EXACT [] xref: EC:3.4 is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0008234 name: cysteine-type peptidase activity namespace: molecular_function alt_id: GO:0004220 def: "Catalysis of the hydrolysis of peptide linkages in oligopeptides or polypeptides; a cysteine residue is at the active center." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "cysteine protease activity" EXACT [] synonym: "thiol protease activity" EXACT [] xref: EC:3.4.-.- is_a: GO:0008233 ! peptidase activity [Term] id: GO:0008236 name: serine-type peptidase activity namespace: molecular_function def: "Catalysis of the hydrolysis of peptide linkages in oligopeptides or polypeptides by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine)." [http://en.wikipedia.org/wiki/Serine_hydrolase, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "serine protease activity" EXACT [] is_a: GO:0008233 ! peptidase activity [Term] id: GO:0008237 name: metallopeptidase activity namespace: molecular_function subset: gosubset_prok subset: PANTHERGOslim xref: Reactome:1795 is_a: GO:0008233 ! peptidase activity [Term] id: GO:0008283 name: cell proliferation namespace: biological_process def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0009987 ! cellular process [Term] id: GO:0008289 name: lipid binding namespace: molecular_function def: "Interacting selectively with a lipid." [GOC:ai] subset: goslim_candida subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005488 ! binding [Term] id: GO:0008324 name: cation transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of cation from one side of the membrane to the other." [GOC:df, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim synonym: "transmembrane cation transporter activity" EXACT [] is_a: GO:0022857 ! transmembrane transporter activity [Term] id: GO:0008415 name: acyltransferase activity namespace: molecular_function def: "Catalysis of the generalized reaction: acyl-carrier + reactant = acyl-reactant + carrier." [EC:2.3.1.-, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim xref: EC:2.3.1.- xref: Reactome:1091 is_a: GO:0016740 ! transferase activity [Term] id: GO:0008483 name: transaminase activity namespace: molecular_function def: "Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "aminotransferase activity" EXACT [] xref: EC:2.6.1 is_a: GO:0016740 ! transferase activity [Term] id: GO:0008632 name: apoptotic program namespace: biological_process def: "The intracellular signaling cascade that results when a cell is triggered to undergo apoptosis." [GOC:go_curators] subset: PANTHERGOslim is_a: GO:0007242 ! intracellular signaling cascade relationship: part_of GO:0006915 ! apoptosis [Term] id: GO:0008643 name: carbohydrate transport namespace: biological_process alt_id: GO:0006861 alt_id: GO:0008644 def: "The directed movement of carbohydrate into, out of, within or between cells. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "sugar transport" NARROW [] is_a: GO:0006810 ! transport [Term] id: GO:0008652 name: amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "amino acid anabolism" EXACT [] synonym: "amino acid biosynthesis" EXACT [] synonym: "amino acid formation" EXACT [] synonym: "amino acid synthesis" EXACT [] is_a: GO:0006520 ! amino acid metabolic process [Term] id: GO:0009008 name: DNA-methyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a methyl group to a DNA molecule." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "deoxyribonucleate methylase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleate methyltransferase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleic acid methylase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleic acid methyltransferase activity" EXACT [EC:2.1.1.-] synonym: "deoxyribonucleic acid modification methylase activity" RELATED [EC:2.1.1.-] synonym: "DNA methylase" BROAD [] synonym: "DNA methyltransferase activity" EXACT [] synonym: "DNA transmethylase activity" EXACT [EC:2.1.1.-] synonym: "Type II DNA methylase" RELATED [EC:2.1.1.37] xref: EC:2.1.1.- is_a: GO:0008168 ! methyltransferase activity [Term] id: GO:0009055 name: electron carrier activity namespace: molecular_function def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport system." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "2Fe-2S electron transfer carrier" NARROW [] synonym: "3Fe-4S/4Fe-4S electron transfer carrier" NARROW [] synonym: "adrenodoxin-type ferredoxin" NARROW [] synonym: "amicyanin" NARROW [] synonym: "azurin" NARROW [] synonym: "bacterial-type ferredoxin" NARROW [] synonym: "chloroplast-type ferredoxin" NARROW [] synonym: "copper electron carrier" NARROW [] synonym: "dicluster bacterial-type ferredoxin" NARROW [] synonym: "electron carrier, chlorophyll electron transport system" RELATED [] synonym: "electron transfer flavoprotein" NARROW [] synonym: "electron transfer flavoprotein, group I" NARROW [] synonym: "electron transfer flavoprotein, group II" NARROW [] synonym: "electron transporter activity" EXACT [] synonym: "high-potential iron-sulfur carrier" NARROW [] synonym: "iron-sulfur electron transfer carrier" NARROW [] synonym: "monocluster bacterial-type ferredoxin" NARROW [] synonym: "mononuclear iron electron carrier" NARROW [] synonym: "polyferredoxin" NARROW [] synonym: "redox-active disulfide bond electron carrier" NARROW [] synonym: "rubredoxin" NARROW [] synonym: "small blue copper electron carrier" NARROW [] synonym: "thioredoxin-like 2Fe-2S ferredoxin" NARROW [] xref: Reactome:20046 is_a: GO:0016491 ! oxidoreductase activity [Term] id: GO:0009056 name: catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "breakdown" EXACT [] synonym: "catabolism" EXACT [] synonym: "degradation" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0009058 name: biosynthetic process namespace: biological_process def: "The energy-requiring part of metabolism in which simpler substances are transformed into more complex ones, as in growth and other biosynthetic processes." [ISBN:0198547684] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "anabolism" EXACT [] synonym: "biosynthesis" EXACT [] synonym: "formation" EXACT [] synonym: "synthesis" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0009063 name: amino acid catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "amino acid breakdown" EXACT [] synonym: "amino acid catabolism" EXACT [] synonym: "amino acid degradation" EXACT [] is_a: GO:0006520 ! amino acid metabolic process [Term] id: GO:0009110 name: vitamin biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "vitamin anabolism" EXACT [] synonym: "vitamin biosynthesis" EXACT [] synonym: "vitamin formation" EXACT [] synonym: "vitamin synthesis" EXACT [] is_a: GO:0006766 ! vitamin metabolic process [Term] id: GO:0009111 name: vitamin catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "vitamin breakdown" EXACT [] synonym: "vitamin catabolism" EXACT [] synonym: "vitamin degradation" EXACT [] is_a: GO:0006766 ! vitamin metabolic process [Term] id: GO:0009187 name: cyclic nucleotide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:go_curators, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "cyclic nucleotide metabolism" EXACT [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0009299 name: mRNA transcription namespace: biological_process def: "The synthesis of messenger RNA (mRNA) from a DNA template." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "mRNA biosynthesis" BROAD [] synonym: "mRNA biosynthetic process" BROAD [] synonym: "mRNA synthesis" BROAD [] is_a: GO:0016070 ! RNA metabolic process [Term] id: GO:0009536 name: plastid namespace: cellular_component def: "Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid." [GOC:jl, ISBN:0198547684] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005575 ! cellular_component [Term] id: GO:0009566 name: fertilization namespace: biological_process def: "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [GOC:tb, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim is_a: GO:0000003 ! reproduction [Term] id: GO:0009579 name: thylakoid namespace: cellular_component def: "A membraneous cellular structure that bears the photosynthetic pigments in photosynthetic organisms. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [GOC:ds, GOC:mtg_sensu, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "photosynthetic membrane" RELATED [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0009605 name: response to external stimulus namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." [GOC:hb] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "response to environmental stimulus" EXACT [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009607 name: response to biotic stimulus namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism." [GOC:hb] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009628 name: response to abiotic stimulus namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." [GOC:hb] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009636 name: response to toxin namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxin stimulus." [GOC:lr] subset: gosubset_prok subset: PANTHERGOslim synonym: "detoxification response" NARROW [] synonym: "toxin resistance" RELATED [] synonym: "toxin susceptibility/resistance" RELATED [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009653 name: anatomical structure morphogenesis namespace: biological_process def: "The process by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125] subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "embryogenesis and morphogenesis" BROAD [] synonym: "morphogenesis" EXACT [] is_a: GO:0032502 ! developmental process [Term] id: GO:0009719 name: response to endogenous stimulus namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an endogenous stimulus." [GOC:sm] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009790 name: embryonic development namespace: biological_process alt_id: GO:0009795 def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] subset: goslim_generic subset: goslim_plant subset: PANTHERGOslim synonym: "embryogenesis" EXACT [] synonym: "embryogenesis and morphogenesis" BROAD [] synonym: "embryonal development" EXACT [] is_a: GO:0032502 ! developmental process [Term] id: GO:0009948 name: anterior/posterior axis specification namespace: biological_process def: "The establishment, maintenance and elaboration of the anterior/posterior axis." [GOC:go_curators] subset: PANTHERGOslim is_a: GO:0007389 ! pattern specification process [Term] id: GO:0009950 name: dorsal/ventral axis specification namespace: biological_process def: "The establishment, maintenance and elaboration of the dorsal/ventral axis." [GOC:go_curators] subset: PANTHERGOslim is_a: GO:0007389 ! pattern specification process [Term] id: GO:0009987 name: cellular process namespace: biological_process alt_id: GO:0008151 alt_id: GO:0050875 def: "Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete] subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0015031 name: protein transport namespace: biological_process alt_id: GO:0015831 def: "The directed movement of proteins into, out of, within or between cells." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "enzyme transport" NARROW [] is_a: GO:0006810 ! transport [Term] id: GO:0015078 name: hydrogen ion transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of hydrogen ions from one side of a membrane to the other." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "proton transporter" EXACT [] xref: Reactome:1383 is_a: GO:0022857 ! transmembrane transporter activity [Term] id: GO:0015144 name: carbohydrate transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of carbohydrate from one side of the membrane to the other." [GOC:jl, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim synonym: "sugar transporter" NARROW [] is_a: GO:0005215 ! transporter activity [Term] id: GO:0015171 name: amino acid transmembrane transporter activity namespace: molecular_function alt_id: GO:0015359 def: "Catalysis of the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and can combine in linear arrays to form proteins in living organisms." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim synonym: "amino acid permease activity" EXACT [] synonym: "amino acid transporter activity" BROAD [] synonym: "amino acid/choline transmembrane transporter activity" NARROW [] synonym: "general amino acid permease activity" RELATED [] synonym: "hydroxy/aromatic amino acid permease activity" NARROW [] is_a: GO:0005215 ! transporter activity [Term] id: GO:0015276 name: ligand-gated ion channel activity namespace: molecular_function def: "Catalysis of the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok subset: PANTHERGOslim synonym: "ionotropic neurotransmitter receptor" NARROW [] is_a: GO:0005216 ! ion channel activity [Term] id: GO:0015464 name: acetylcholine receptor activity namespace: molecular_function def: "Combining with acetylcholine to initiate a change in cell activity." [GOC:jl] subset: PANTHERGOslim is_a: GO:0004872 ! receptor activity [Term] id: GO:0015629 name: actin cytoskeleton namespace: cellular_component def: "The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes." [GOC:jl, http://cancerweb.ncl.ac.uk/, ISBN:0395825172] subset: PANTHERGOslim is_a: GO:0005856 ! cytoskeleton [Term] id: GO:0015925 name: galactosidase activity namespace: molecular_function def: "Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.2.1.- is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds [Term] id: GO:0015926 name: glucosidase activity namespace: molecular_function def: "Catalysis of the hydrolysis of glucosyl compounds, substances containing a group derived from a cyclic form of glucose or a glucose derivative." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.2.1.- is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds [Term] id: GO:0015931 name: nucleobase, nucleoside, nucleotide and nucleic acid transport namespace: biological_process def: "The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of, within or between cells." [GOC:ai] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0016023 name: cytoplasmic membrane-bounded vesicle namespace: cellular_component def: "A membrane-bounded vesicle found in the cytoplasm of the cell." [GOC:ai, GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "cytoplasmic membrane bounded vesicle" EXACT [] synonym: "cytoplasmic membrane-enclosed vesicle" EXACT [] is_a: GO:0043226 ! organelle relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0016032 name: viral reproduction namespace: biological_process def: "The process by which a virus reproduces. Usually, this is by infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle." [GOC:mah] comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'. subset: goslim_generic subset: goslim_pir subset: PANTHERGOslim synonym: "viral infection" RELATED [] synonym: "viral life cycle" EXACT [] synonym: "viral replication cycle" EXACT [] synonym: "virulence" RELATED [] xref: Reactome:162587 xref: Reactome:162906 xref: Reactome:168255 is_a: GO:0008150 ! biological_process [Term] id: GO:0016043 name: cellular component organization and biogenesis namespace: biological_process def: "A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a cellular component; includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "cell organisation and biogenesis" EXACT [] synonym: "cell organization and biogenesis" EXACT [] is_a: GO:0008150 ! biological_process is_a: GO:0009987 ! cellular process [Term] id: GO:0016049 name: cell growth namespace: biological_process def: "The process by which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "cell expansion" RELATED [] synonym: "cellular growth" EXACT [] synonym: "growth of cell" EXACT [] synonym: "metabolic process resulting in cell growth" RELATED [] synonym: "metabolism resulting in cell growth" RELATED [] is_a: GO:0009987 ! cellular process is_a: GO:0040007 ! growth [Term] id: GO:0016070 name: RNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "RNA metabolism" EXACT [] is_a: GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0016072 name: rRNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving rRNA, ribosomal RNA, a structural constituent of ribosomes." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "rRNA metabolism" EXACT [] is_a: GO:0016070 ! RNA metabolic process [Term] id: GO:0016079 name: synaptic vesicle exocytosis namespace: biological_process def: "Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft." [GOC:jic, GOC:lmg] subset: PANTHERGOslim is_a: GO:0006887 ! exocytosis relationship: part_of GO:0007269 ! neurotransmitter secretion [Term] id: GO:0016160 name: amylase activity namespace: molecular_function def: "Catalysis of the hydrolysis of amylose or an amylose derivative." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.2.1.- is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds [Term] id: GO:0016170 name: interleukin-15 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-15 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-15" NARROW [] synonym: "interleukin-15 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0016192 name: vesicle-mediated transport namespace: biological_process alt_id: GO:0006899 def: "The directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell." [GOC:ai] subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "nonselective vesicle transport" NARROW [] synonym: "synaptic vesicle fission" RELATED [] synonym: "synaptic vesicle fusion" RELATED [] synonym: "synaptic vesicle internalization" RELATED [] synonym: "synaptic vesicle retrieval" RELATED [] synonym: "vesicle trafficking" RELATED [] synonym: "vesicle transport" EXACT [] is_a: GO:0006810 ! transport [Term] id: GO:0016209 name: antioxidant activity namespace: molecular_function def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003674 ! molecular_function [Term] id: GO:0016265 name: death namespace: biological_process def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099] comment: See also the biological process term 'apoptosis ; GO:0006915'. subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0032502 ! developmental process [Term] id: GO:0016298 name: lipase activity namespace: molecular_function def: "Catalysis of the hydrolysis of a lipid or phospholipid." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.1.1.- xref: Reactome:1913 is_a: GO:0016788 ! hydrolase activity, acting on ester bonds [Term] id: GO:0016301 name: kinase activity namespace: molecular_function def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "phosphokinase activity" EXACT [] xref: Reactome:1423 is_a: GO:0016740 ! transferase activity [Term] id: GO:0016337 name: cell-cell adhesion namespace: biological_process def: "The attachment of one cell to another cell via adhesion molecules." [GOC:hb] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0007155 ! cell adhesion [Term] id: GO:0016407 name: acetyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of an acetyl group to an acceptor molecule." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim synonym: "acetylase activity" EXACT [] xref: EC:2.3.1.- xref: Reactome:1621 is_a: GO:0008415 ! acyltransferase activity [Term] id: GO:0016462 name: pyrophosphatase activity namespace: molecular_function def: "Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments." [EC:3.6.1.-, http://cancerweb.ncl.ac.uk/] subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.6.1.- xref: Reactome:3222 is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0016491 name: oxidoreductase activity namespace: molecular_function def: "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:go_curators] comment: Note that enzymes of class EC:1.97.-.- should also be annotated to this term. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "oxidoreductase activity, acting on other substrates" NARROW [] synonym: "redox activity" EXACT [] xref: EC:1 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016740 name: transferase activity namespace: molecular_function def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim xref: EC:2 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016757 name: transferase activity, transferring glycosyl groups namespace: molecular_function alt_id: GO:0016932 def: "Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that enzymes of class EC:2.4.99.- should also be annotated to this term. subset: gosubset_prok subset: PANTHERGOslim synonym: "glycosyltransferase activity" EXACT [] synonym: "transferase activity, transferring other glycosyl groups" NARROW [] synonym: "transglycosylase activity" EXACT [] xref: EC:2.4 is_a: GO:0016740 ! transferase activity [Term] id: GO:0016779 name: nucleotidyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim xref: EC:2.7.7 is_a: GO:0016740 ! transferase activity [Term] id: GO:0016787 name: hydrolase activity namespace: molecular_function def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim xref: EC:3 xref: Reactome:450 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016788 name: hydrolase activity, acting on ester bonds namespace: molecular_function def: "Catalysis of the hydrolysis of any ester bond." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "esterase activity" EXACT [] xref: EC:3.1 xref: Reactome:448 is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0016791 name: phosphoric monoester hydrolase activity namespace: molecular_function alt_id: GO:0016302 def: "Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate." [http://cancerweb.ncl.ac.uk/] subset: gosubset_prok subset: PANTHERGOslim synonym: "phosphatase" RELATED [] synonym: "phosphatase activity" EXACT [] xref: EC:3.1.3 is_a: GO:0016787 ! hydrolase activity is_a: GO:0016788 ! hydrolase activity, acting on ester bonds [Term] id: GO:0016799 name: hydrolase activity, hydrolyzing N-glycosyl compounds namespace: molecular_function def: "Catalysis of the hydrolysis of any N-glycosyl bond." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim xref: EC:3.2.2 is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0016829 name: lyase activity namespace: molecular_function def: "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC:4.-.-.-, ISBN:0198547684] comment: Note that enzymes of class EC:4.99.-.- should also be annotated to this term. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "other lyase activity" NARROW [] xref: EC:4 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016831 name: carboxy-lyase activity namespace: molecular_function def: "Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound." [http://www.mercksource.com/] subset: gosubset_prok subset: PANTHERGOslim synonym: "decarboxylase activity" EXACT [] xref: EC:4.1.1 xref: Reactome:1605 is_a: GO:0016829 ! lyase activity [Term] id: GO:0016832 name: aldehyde-lyase activity namespace: molecular_function alt_id: GO:0016228 def: "Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone." [http://www.mercksource.com/] subset: gosubset_prok subset: PANTHERGOslim synonym: "aldolase activity" BROAD [] xref: EC:4.1.2 is_a: GO:0016829 ! lyase activity [Term] id: GO:0016836 name: hydro-lyase activity namespace: molecular_function def: "Catalysis of the cleavage of a carbon-oxygen bond by elimination of water." [EC:4.2.1] subset: gosubset_prok subset: PANTHERGOslim xref: EC:4.2.1 is_a: GO:0016829 ! lyase activity [Term] id: GO:0016853 name: isomerase activity namespace: molecular_function def: "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that enzymes of class EC:5.99.-.- should also be annotated to this term. subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "other isomerase activity" NARROW [] xref: EC:5 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016854 name: racemase and epimerase activity namespace: molecular_function def: "Catalysis of a reaction that alters the configuration of one or more chiral centers in a molecule." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that enzymes of class EC:5.1.99.- should also be annotated to this term. Note that 'epimerase' refers to the conversion of an epimer into its diastereoisomer, and 'racemase' refers to the interconversion of the two enantiomers of a chiral compound. subset: gosubset_prok subset: PANTHERGOslim synonym: "racemase and epimerase activity, acting on other compounds" NARROW [] xref: EC:5.1 is_a: GO:0016853 ! isomerase activity [Term] id: GO:0016866 name: intramolecular transferase activity namespace: molecular_function def: "Catalysis of the transfer of a functional group from one position to another within a single molecule." [GOC:mah] comment: Note that enzymes of class EC:5.4.99.- should also be annotated to this term. subset: gosubset_prok subset: PANTHERGOslim synonym: "intramolecular transferase activity, transferring other groups" NARROW [] synonym: "mutase activity" EXACT [] xref: EC:5.4 is_a: GO:0016853 ! isomerase activity [Term] id: GO:0016874 name: ligase activity namespace: molecular_function def: "Catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_candida subset: goslim_goa subset: goslim_pir subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim xref: EC:6 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016917 name: GABA receptor activity namespace: molecular_function def: "Combining with gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, to initiate a change in cell activity." [GOC:jl, http://cancerweb.ncl.ac.uk/] comment: See also the molecular function term 'neurotransmitter receptor activity ; GO:0030594'. subset: PANTHERGOslim synonym: "4-aminobutanoate receptor activity" EXACT [] synonym: "4-aminobutyrate receptor activity" EXACT [] synonym: "GABA binding" EXACT [] synonym: "gamma-aminobutyrate binding" EXACT [] synonym: "gamma-aminobutyric acid binding" EXACT [] synonym: "gamma-aminobutyric acid receptor activity" EXACT [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0019104 name: DNA N-glycosylase activity namespace: molecular_function alt_id: GO:0008578 def: "Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site." [GOC:elh, PMID:11554296] comment: Consider also annotating to the molecular function term 'damaged DNA binding ; GO:0003684'. subset: gosubset_prok subset: PANTHERGOslim synonym: "DNA glycosylase activity" EXACT [] synonym: "endonuclease VIII activity" RELATED [] xref: EC:3.2.2.- xref: Reactome:7370 is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds [Term] id: GO:0019199 name: transmembrane receptor protein kinase activity namespace: molecular_function subset: gosubset_prok subset: PANTHERGOslim xref: EC:2.7.11.- is_a: GO:0004672 ! protein kinase activity is_a: GO:0004872 ! receptor activity [Term] id: GO:0019200 name: carbohydrate kinase activity namespace: molecular_function def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a carbohydrate substrate molecule." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0016301 ! kinase activity [Term] id: GO:0019201 name: nucleotide kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + nucleoside monophosphate = ADP + nucleoside diphosphate." [GOC:ai, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0016301 ! kinase activity [Term] id: GO:0019202 name: amino acid kinase activity namespace: molecular_function def: "Catalysis of the transfer of a phosphate group, usually from ATP, to an amino acid substrate." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0016301 ! kinase activity [Term] id: GO:0019203 name: carbohydrate phosphatase activity namespace: molecular_function def: "Catalysis of the reaction: carbohydrate phosphate + H2O = carbohydrate + phosphate." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0016791 ! phosphoric monoester hydrolase activity [Term] id: GO:0019204 name: nucleotide phosphatase activity namespace: molecular_function subset: PANTHERGOslim is_a: GO:0016791 ! phosphoric monoester hydrolase activity [Term] id: GO:0019207 name: kinase regulator activity namespace: molecular_function def: "Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0030234 ! enzyme regulator activity [Term] id: GO:0019208 name: phosphatase regulator activity namespace: molecular_function def: "Modulates the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai] subset: PANTHERGOslim is_a: GO:0030234 ! enzyme regulator activity [Term] id: GO:0019209 name: kinase activator activity namespace: molecular_function def: "Increases the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0008047 ! enzyme activator activity is_a: GO:0019207 ! kinase regulator activity [Term] id: GO:0019210 name: kinase inhibitor activity namespace: molecular_function def: "Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0004857 ! enzyme inhibitor activity is_a: GO:0019207 ! kinase regulator activity [Term] id: GO:0019211 name: phosphatase activator activity namespace: molecular_function def: "Increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai] subset: PANTHERGOslim is_a: GO:0008047 ! enzyme activator activity is_a: GO:0019208 ! phosphatase regulator activity [Term] id: GO:0019212 name: phosphatase inhibitor activity namespace: molecular_function def: "Stops, prevents or reduces the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai] subset: PANTHERGOslim is_a: GO:0004857 ! enzyme inhibitor activity is_a: GO:0019208 ! phosphatase regulator activity [Term] id: GO:0019213 name: deacetylase activity namespace: molecular_function def: "Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." [GOC:jl] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0019215 name: intermediate filament binding namespace: molecular_function def: "Interacting selectively with an intermediate filament, a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim is_a: GO:0008092 ! cytoskeletal protein binding [Term] id: GO:0019219 name: regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] subset: gosubset_prok subset: PANTHERGOslim synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] relationship: regulates GO:0006139 ! nucleobase, nucleoside, nucleotide and nucleic acid metabolic process [Term] id: GO:0019220 name: regulation of phosphate metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators] subset: gosubset_prok subset: PANTHERGOslim synonym: "regulation of phosphate metabolism" EXACT [] relationship: regulates GO:0006796 ! phosphate metabolic process [Term] id: GO:0019221 name: cytokine and chemokine mediated signaling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of a cytokine or chemokine binding to a cell surface receptor." [GOC:mah] subset: PANTHERGOslim synonym: "cytokine and chemokine mediated signalling pathway" EXACT [] is_a: GO:0007166 ! cell surface receptor linked signal transduction [Term] id: GO:0019227 name: action potential propagation namespace: biological_process def: "A neurological process that causes the sequential depolarization of a neuron's cell membrane along an axon." [GOC:isa_complete] subset: PANTHERGOslim is_a: GO:0050877 ! neurological system process [Term] id: GO:0019229 name: regulation of vasoconstriction namespace: biological_process def: "Any process that modulates the frequency, rate or extent of reductions in the diameter of blood vessels." [GOC:jl] subset: PANTHERGOslim is_a: GO:0050789 ! regulation of biological process [Term] id: GO:0019233 name: sensory perception of pain namespace: biological_process def: "The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances." [http://www.onelook.com/] subset: PANTHERGOslim synonym: "nociception" EXACT [] synonym: "perception of physiological pain" NARROW [] is_a: GO:0007600 ! sensory perception [Term] id: GO:0019236 name: response to pheromone namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "pheromone response" EXACT [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0019237 name: centromeric DNA binding namespace: molecular_function def: "Interacting selectively with centromere-associated DNA, usually characterized by highly repetitive sequences." [GOC:jl, ISBN:0321000382] subset: PANTHERGOslim synonym: "centromere binding" BROAD [] is_a: GO:0003677 ! DNA binding [Term] id: GO:0019239 name: deaminase activity namespace: molecular_function def: "Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3)." [GOC:jl, http://cancerweb.ncl.ac.uk/] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003824 ! catalytic activity [Term] id: GO:0019538 name: protein metabolic process namespace: biological_process alt_id: GO:0006411 def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification." [GOC:ma] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "protein metabolic process and modification" EXACT [] synonym: "protein metabolism" EXACT [] synonym: "protein metabolism and modification" EXACT [] is_a: GO:0044238 ! primary metabolic process [Term] id: GO:0019722 name: calcium-mediated signaling namespace: biological_process def: "A series of molecular signals in which a cell uses calcium ions to convert an extracellular signal into a response." [GOC:ceb] subset: PANTHERGOslim synonym: "calcium signaling" EXACT [] synonym: "calcium signalling" EXACT [] synonym: "calcium-mediated signalling" EXACT [] is_a: GO:0007242 ! intracellular signaling cascade [Term] id: GO:0019724 name: B cell mediated immunity namespace: biological_process def: "Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells." [GOC:add, GOC:mtg_15nov05, ISBN:0781735149 "Fundamental Immunology"] comment: This term was improved by GO_REF:0000022. It was moved. subset: PANTHERGOslim synonym: "B lymphocyte mediated immune effector process" EXACT [] synonym: "B lymphocyte mediated immunity" EXACT [] synonym: "B-cell mediated immune effector process" EXACT [] synonym: "B-cell mediated immunity" EXACT [] synonym: "B-lymphocyte mediated immune effector process" EXACT [] synonym: "B-lymphocyte mediated immunity" EXACT [] is_a: GO:0006955 ! immune response [Term] id: GO:0019740 name: nitrogen utilization namespace: biological_process subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0019748 name: secondary metabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "secondary metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0019763 name: immunoglobulin receptor activity namespace: molecular_function alt_id: GO:0016489 def: "Combining with the Fc region of an immunoglobulin protein to initiate a change in cell activity." [ISBN:0198547684] subset: PANTHERGOslim synonym: "FC receptor activity" EXACT [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0019814 name: immunoglobulin complex namespace: cellular_component def: "A multiprotein complex that functions as an antibody. Immunoglobulins (Igs) are composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. The classes of Ig are IgA, IgD, IgE, IgG and IgM; they may be embedded in the plasma membrane or circulate in the blood or lymph." [GOC:jl, ISBN:0140512713] subset: goslim_pir subset: PANTHERGOslim is_a: GO:0043234 ! protein complex [Term] id: GO:0019825 name: oxygen binding namespace: molecular_function def: "Interacting selectively with oxygen (O2)." [GOC:jl] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "cytochrome P450" NARROW [] synonym: "cytochrome P450 activity" RELATED [] xref: Reactome:4477 is_a: GO:0005488 ! binding [Term] id: GO:0019882 name: antigen processing and presentation namespace: biological_process alt_id: GO:0030333 def: "The process by which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [GOC:add, GOC:mtg_15nov05, ISBN:0781735149 "Fundamental Immunology", PMID:15771591, PMID:15928678] comment: This term was improved by GO_REF:0000022. It was renamed and redefined. subset: PANTHERGOslim synonym: "antigen presentation" EXACT [] synonym: "antigen processing" EXACT [] is_a: GO:0002376 ! immune system process [Term] id: GO:0019911 name: structural constituent of myelin sheath namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the myelin sheath of a nerve." [GOC:mah] subset: PANTHERGOslim is_a: GO:0005198 ! structural molecule activity [Term] id: GO:0022857 name: transmembrane transporter activity namespace: molecular_function alt_id: GO:0005386 alt_id: GO:0015646 def: "Catalysis of the transfer of a substance from one side of a membrane to the other." [GOC:mtg_transport, ISBN:0815340729] subset: PANTHERGOslim is_a: GO:0005215 ! transporter activity [Term] id: GO:0022904 name: respiratory electron transport chain namespace: biological_process def: "A process whereby a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [GOC:mtg_electron_transport, http://cancerweb.ncl.ac.uk/] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "6-phosphofructokinase reduction" RELATED [] synonym: "dihydrobiopterin reduction" RELATED [] synonym: "dihydrolipoamide reduction" RELATED [] synonym: "dihydrolipoylprotein reduction" RELATED [] synonym: "dihydropteridine reduction" RELATED [] synonym: "electron transfer" EXACT [] synonym: "other pathways of electron transport" RELATED [] synonym: "oxidized glutathione reduction" RELATED [] synonym: "protein-disulfide reduction" RELATED [] is_a: GO:0006091 ! generation of precursor metabolites and energy [Term] id: GO:0030054 name: cell junction namespace: cellular_component def: "A specialized region of connection between two cells or between a cell and the extracellular matrix." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim relationship: part_of GO:0005886 ! plasma membrane [Term] id: GO:0030097 name: hemopoiesis namespace: biological_process def: "The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates." [GOC:dgh, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "blood cell biosynthesis" EXACT [] synonym: "blood cell formation" EXACT [] synonym: "haemopoiesis" EXACT [] synonym: "hematopoiesis" EXACT [] is_a: GO:0048731 ! system development [Term] id: GO:0030101 name: natural killer cell activation namespace: biological_process def: "The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735140] subset: PANTHERGOslim synonym: "NK cell activation" EXACT [] is_a: GO:0006955 ! immune response [Term] id: GO:0030120 name: vesicle coat namespace: cellular_component def: "A membrane coat found on a coated vesicle." [GOC:mah] subset: PANTHERGOslim relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0030154 name: cell differentiation namespace: biological_process def: "The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_goa subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0032502 ! developmental process [Term] id: GO:0030188 name: chaperone regulator activity namespace: molecular_function def: "Modulates the activity of a molecular chaperone." [GOC:mah] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003674 ! molecular_function [Term] id: GO:0030234 name: enzyme regulator activity namespace: molecular_function def: "Modulates the activity of an enzyme." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "enzyme modulator" EXACT [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0030246 name: carbohydrate binding namespace: molecular_function def: "Interacting selectively with any carbohydrate." [GOC:mah] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "selectin" RELATED [] is_a: GO:0005488 ! binding [Term] id: GO:0030312 name: external encapsulating structure namespace: cellular_component def: "A structure that lies outside the plasma membrane and surrounds the entire cell." [GOC:go_curators] subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005575 ! cellular_component [Term] id: GO:0030313 name: cell envelope namespace: cellular_component def: "Everything external to, but not including, the cytoplasmic membrane of bacteria, encompassing the periplasmic space, cell wall, and outer membrane if present." [GOC:jl, http://pathmicro.med.sc.edu/fox/cell_envelope.htm] subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0030312 ! external encapsulating structure [Term] id: GO:0030337 name: DNA polymerase processivity factor activity namespace: molecular_function def: "An accessory subunit of DNA polymerase that acts to increase the processivity of polymerization." [UniProtKB:P28958] subset: gosubset_prok subset: PANTHERGOslim synonym: "processivity clamp" EXACT [] synonym: "sliding clamp" EXACT [] is_a: GO:0030234 ! enzyme regulator activity [Term] id: GO:0030367 name: interleukin-17 receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-17 receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-17" NARROW [] synonym: "interleukin-17 receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0030380 name: interleukin-17E receptor binding namespace: molecular_function def: "Interacting selectively with the interleukin-17E receptor." [GOC:ai] subset: PANTHERGOslim synonym: "IL-17E" NARROW [] synonym: "interleukin-17E receptor ligand" NARROW [] is_a: GO:0005126 ! hematopoietin/interferon-class (D200-domain) cytokine receptor binding [Term] id: GO:0030414 name: protease inhibitor activity namespace: molecular_function def: "Stops, prevents or reduces the activity of a protease, any enzyme catalyzes the hydrolysis peptide bonds." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "peptidase inhibitor" EXACT [] is_a: GO:0004857 ! enzyme inhibitor activity [Term] id: GO:0030528 name: transcription regulator activity namespace: molecular_function def: "Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor." [GOC:mah] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "transcriptional regulator activity" EXACT [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0030529 name: ribonucleoprotein complex namespace: cellular_component def: "A macromolecular complex containing both protein and RNA molecules." [GOC:krc] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "protein-RNA complex" EXACT [] synonym: "ribonucleoprotein" EXACT [] synonym: "RNA-protein complex" EXACT [] synonym: "RNP" EXACT [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0030533 name: triplet codon-amino acid adaptor activity namespace: molecular_function def: "The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis." [GOC:hjd, GOC:mtg_MIT, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] comment: Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'. subset: goslim_candida subset: goslim_generic subset: goslim_yeast subset: PANTHERGOslim synonym: "transfer RNA" RELATED [] synonym: "tRNA" RELATED [] is_a: GO:0003723 ! RNA binding [Term] id: GO:0030879 name: mammary gland development namespace: biological_process def: "The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." [PMID:9576833] subset: PANTHERGOslim is_a: GO:0048731 ! system development [Term] id: GO:0031012 name: extracellular matrix namespace: cellular_component def: "A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as in plants)." [GOC:mah] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim relationship: part_of GO:0005576 ! extracellular region [Term] id: GO:0031124 name: mRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of an mRNA molecule." [GOC:mah] subset: gosubset_prok subset: PANTHERGOslim synonym: "mRNA 3' end processing" EXACT [] is_a: GO:0006397 ! mRNA processing [Term] id: GO:0031201 name: SNARE complex namespace: cellular_component def: "A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25." [PMID:10872468] subset: PANTHERGOslim is_a: GO:0043234 ! protein complex [Term] id: GO:0031202 name: RNA splicing factor activity, transesterification mechanism namespace: molecular_function alt_id: GO:0000385 def: "An activity which binds RNA and functions to assist splicing of substrate RNA(s) by facilitating the formation and stabilization of a catalytic conformation in which the splice junctions of the RNA(s) to be spliced are positioned for a transesterification reaction that occurs between two sites within the RNA(s) to be spliced." [GOC:krc] comment: Note that nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism. subset: PANTHERGOslim synonym: "pre-mRNA splicing factor activity" RELATED [] synonym: "spliceosomal catalysis" EXACT [] xref: Reactome:160901 is_a: GO:0003824 ! catalytic activity [Term] id: GO:0031386 name: protein tag namespace: molecular_function def: "Acting as an indicator or marker to facilitate recognition by other molecules in the cell. Recognition of the tag, which can be covalently attached to the target molecule, may result in modification, sequestration, transport or degradation of the molecule in question." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: PANTHERGOslim synonym: "protein tagging activity" RELATED [] synonym: "ubiquitin" RELATED [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0031497 name: chromatin assembly namespace: biological_process def: "The assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html] subset: PANTHERGOslim is_a: GO:0006996 ! organelle organization and biogenesis [Term] id: GO:0032393 name: MHC class I receptor activity namespace: molecular_function def: "Combining with an MHC class I protein complex to initiate a change in cellular activity. Class I here refers to classical class I molecules." [GOC:add, ISBN:0781735149 "Fundamental Immunology"] comment: Note that this term is intended for annotation of gene products that act as receptors for MHC class I protein complexes, not for components of the MHC class I protein complexes themselves. subset: PANTHERGOslim synonym: "alpha-beta T cell receptor activity" RELATED [] synonym: "gamma-delta T cell receptor activity" RELATED [] synonym: "T cell receptor activity" RELATED [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0032394 name: MHC class Ib receptor activity namespace: molecular_function def: "Combining with an MHC class Ib protein complex to initiate a change in cellular activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families." [GOC:add, ISBN:0781735149 "Fundamental Immunology"] comment: Note that this term is intended for annotation of gene products that act as receptors for MHC class Ib protein complexes, not for components of the MHC class Ib protein complexes themselves. subset: PANTHERGOslim synonym: "alpha-beta T cell receptor activity" RELATED [] synonym: "gamma-delta T cell receptor activity" RELATED [] synonym: "T cell receptor activity" RELATED [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0032395 name: MHC class II receptor activity namespace: molecular_function def: "Combining with an MHC class II protein complex to initiate a change in cellular activity." [GOC:add, ISBN:0781735149 "Fundamental Immunology"] comment: Note that this term is intended for annotation of gene products that act as receptors for MHC class II protein complexes, not for components of the MHC class II protein complexes themselves. subset: PANTHERGOslim synonym: "alpha-beta T cell receptor activity" RELATED [] synonym: "gamma-delta T cell receptor activity" RELATED [] synonym: "T cell receptor activity" RELATED [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0032502 name: developmental process namespace: biological_process def: "A biological process whose specific outcome is the progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "development" NARROW [] is_a: GO:0008150 ! biological_process [Term] id: GO:0032543 name: mitochondrial translation namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:go_curators] subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "mitochondrial protein anabolism" EXACT [] synonym: "mitochondrial protein biosynthesis" EXACT [] synonym: "mitochondrial protein formation" EXACT [] synonym: "mitochondrial protein synthesis" EXACT [] synonym: "mitochondrial protein translation" EXACT [] is_a: GO:0006412 ! translation is_a: GO:0007005 ! mitochondrion organization and biogenesis [Term] id: GO:0032544 name: plastid translation namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a protein in a plastid. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the plastid has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:go_curators] subset: goslim_generic subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim synonym: "plastid protein anabolism" EXACT [] synonym: "plastid protein biosynthesis" EXACT [] synonym: "plastid protein formation" EXACT [] synonym: "plastid protein synthesis" EXACT [] synonym: "plastid protein translation" EXACT [] is_a: GO:0006412 ! translation [Term] id: GO:0032568 name: general transcription from RNA polymerase II promoter namespace: biological_process def: "The basal, non-specifically regulated synthesis of RNA from a DNA template by RNA polymerase II (Pol II), originating at a Pol II-specific promoter. Mediated by core RNA polymerase II and a set of general transcription factors; in Saccharomyces five transcription factors are necessary and sufficient for such basal transcription." [GOC:mah] subset: PANTHERGOslim is_a: GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0032791 name: lead ion binding namespace: molecular_function def: "Interacting selectively with lead (Pb) ions." [GOC:mah] subset: goslim_generic subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005488 ! binding [Term] id: GO:0032989 name: cellular structure morphogenesis namespace: biological_process def: "The process by which cellular structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:mah] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0009653 ! anatomical structure morphogenesis is_a: GO:0016043 ! cellular component organization and biogenesis [Term] id: GO:0034341 name: response to interferon-gamma namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon." [GOC:add, ISBN:0126896631, PMID:15546383] subset: PANTHERGOslim synonym: "response to gamma-interferon" RELATED [] synonym: "response to immune interferon" EXACT [] synonym: "response to type II IFN" EXACT [] synonym: "response to type II interferon" EXACT [] is_a: GO:0006955 ! immune response [Term] id: GO:0040007 name: growth namespace: biological_process def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] comment: See also the biological process term 'cell growth ; GO:0016049'. subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim synonym: "growth pattern" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0040029 name: regulation of gene expression, epigenetic namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582] subset: goslim_generic subset: goslim_plant subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0050789 ! regulation of biological process [Term] id: GO:0042116 name: macrophage activation namespace: biological_process def: "A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735149 "Fundamental Immunology", PMID:14506301] subset: PANTHERGOslim is_a: GO:0002376 ! immune system process [Term] id: GO:0042558 name: pteridine and derivative metabolic process namespace: biological_process alt_id: GO:0019721 def: "The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid." [GOC:jl, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok subset: PANTHERGOslim synonym: "pteridine and derivative metabolism" EXACT [] synonym: "pterin metabolic process" EXACT [] synonym: "pterin metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0042592 name: homeostatic process namespace: biological_process def: "The biological processes involved in the maintenance of an internal equilibrium." [GOC:jl, ISBN:0395825172] subset: gosubset_prok subset: PANTHERGOslim synonym: "homeostasis" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0042611 name: MHC protein complex namespace: cellular_component def: "A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen." [GOC:add, GOC:jl, ISBN:0781735149 "Fundamental Immunology", PMID:15928678, PMID:16153240] subset: goslim_pir subset: PANTHERGOslim is_a: GO:0043234 ! protein complex [Term] id: GO:0042626 name: ATPase activity, coupled to transmembrane movement of substances namespace: molecular_function def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate to directly drive the active transport of a substance across a membrane." [EC:3.6.1.3, GOC:jl] comment: Consider also annotating to the molecular function term 'ATP binding ; GO:0005524'. subset: gosubset_prok subset: PANTHERGOslim synonym: "ABC transporter" NARROW [] synonym: "ABC-type efflux permease activity" NARROW [] synonym: "ABC-type efflux porter activity" NARROW [] synonym: "ABC-type uptake permease activity" NARROW [] synonym: "ATP binding cassette transporter" NARROW [] synonym: "ATP-binding cassette (ABC) transporter activity" NARROW [] synonym: "ATP-binding cassette transporter" NARROW [] synonym: "mating pheromone exporter" NARROW [] is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0042742 name: defense response to bacterium namespace: biological_process alt_id: GO:0042830 def: "Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "antibacterial peptide activity" RELATED [] synonym: "defence response to bacteria" EXACT [] synonym: "defence response to bacterium" EXACT [] synonym: "defense response to bacteria" EXACT [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0043066 name: negative regulation of apoptosis namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cell death by apoptosis." [GOC:jl] subset: PANTHERGOslim synonym: "down regulation of apoptosis" EXACT [] synonym: "down-regulation of apoptosis" EXACT [] synonym: "downregulation of apoptosis" EXACT [] synonym: "inhibition of apoptosis" NARROW [] relationship: negatively_regulates GO:0006915 ! apoptosis [Term] id: GO:0043226 name: organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim relationship: part_of GO:0005622 ! intracellular [Term] id: GO:0043234 name: protein complex namespace: cellular_component def: "Any protein group composed of two or more subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." [GOC:go_curators] comment: Note that although at some level almost all cellular components can be thought of as protein complexes, this term is intended to exclude structures composed of the same repeating subunit or subunits, for example microtubules. Protein complexes encompassed by this term are generally not structural, and usually have a defined set of subunits. subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0005575 ! cellular_component [Term] id: GO:0043574 name: peroxisomal transport namespace: biological_process def: "Transport of substances into, out of or within a peroxisome, a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC:jl] subset: PANTHERGOslim is_a: GO:0006810 ! transport [Term] id: GO:0043855 name: cyclic nucleotide-gated ion channel activity namespace: molecular_function def: "Catalysis of the transmembrane transfer of an ion by a channel that opens when a cyclic nucleotide has been bound by the channel complex or one of its constituent parts." [GOC:jl] subset: gosubset_prok subset: PANTHERGOslim synonym: "cyclic nucleotide activated ion channel activity" EXACT [] synonym: "cyclic nucleotide gated ion channel activity" EXACT [] synonym: "cyclic nucleotide-activated ion channel activity" EXACT [] is_a: GO:0015276 ! ligand-gated ion channel activity [Term] id: GO:0044238 name: primary metabolic process namespace: biological_process def: "Reactions involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "primary metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0045111 name: intermediate filament cytoskeleton namespace: cellular_component def: "Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell." [ISBN:0716731363] subset: PANTHERGOslim is_a: GO:0005856 ! cytoskeleton [Term] id: GO:0045182 name: translation regulator activity namespace: molecular_function def: "Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai] subset: goslim_candida subset: goslim_generic subset: goslim_goa subset: goslim_pir subset: goslim_plant subset: goslim_yeast subset: gosubset_prok subset: PANTHERGOslim is_a: GO:0003674 ! molecular_function [Term] id: GO:0045233 name: natural killer cell receptor activity namespace: molecular_function def: "A receptor found on the surface of natural killer cells which binds Class I MHC antigens and is required for activation of NK activity. It belongs to the Ly49i family." [GOC:ebc] subset: PANTHERGOslim synonym: "Ly49i" NARROW [] synonym: "NK cell receptor activity" EXACT [] is_a: GO:0004872 ! receptor activity [Term] id: GO:0045259 name: proton-transporting ATP synthase complex namespace: cellular_component alt_id: GO:0045255 def: "A proton-transporting two-sector ATPase complex that catalyzes the phosphorylation of ADP to ATP during oxidative phosphorylation. The complex comprises a membrane sector (F0) that carries out proton transport and a cytoplasmic compartment sector (F1) that catalyzes ATP synthesis by a rotational mechanism; the extramembrane sector (containing 3 a and 3 b subunits) is connected via the d-subunit to the membrane sector by several smaller subunits. Within this complex, the g and e subunits and the 9-12 c subunits rotate by consecutive 120 degree angles and perform parts of ATP synthesis. This movement is driven by the hydrogen ion electrochemical potential gradient." [EC:3.6.3.14, ISBN:0198547684, ISBN:0716743663] subset: gosubset_prok subset: PANTHERGOslim synonym: "hydrogen-translocating F-type ATPase complex" EXACT [] synonym: "hydrogen-transporting ATP synthase complex" EXACT [] synonym: "proton-transporting F-type ATPase complex" RELATED [] relationship: part_of GO:0005622 ! intracellular [Term] id: GO:0045298 name: tubulin complex namespace: cellular_component def: "A heterodimer of tubulins alpha and beta that constitutes the protomer for microtubule assembly." [http://cancerweb.ncl.ac.uk/, ISBN:0716731363] subset: PANTHERGOslim is_a: GO:0043234 ! protein complex relationship: part_of GO:0005874 ! microtubule [Term] id: GO:0045735 name: nutrient reservoir activity namespace: molecular_function def: "Functions in the storage of nutritious substrates." [GOC:ai] comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'. subset: goslim_generic subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "storage protein" RELATED [] synonym: "storage protein of fat body (sensu Insecta)" RELATED [] synonym: "yolk protein" RELATED [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0046933 name: hydrogen ion transporting ATP synthase activity, rotational mechanism namespace: molecular_function def: "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ADP + phosphate = ATP + H2O, coupled with transport of H+ down a concentration gradient, by a rotational mechanism." [EC:3.6.3.14, TC:3.A.2.1.1] subset: gosubset_prok subset: PANTHERGOslim synonym: "H+-transporting ATP synthase activity" EXACT [EC:3.6.3.14] synonym: "hydrogen ion translocating F-type ATPase activity" EXACT [] synonym: "hydrogen ion transporting two-sector ATPase activity" EXACT [] xref: Reactome:78757 is_a: GO:0015078 ! hydrogen ion transmembrane transporter activity [Term] id: GO:0048731 name: system development namespace: biological_process def: "The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." [GOC:dph, GOC:jic] subset: PANTHERGOslim is_a: GO:0032502 ! developmental process [Term] id: GO:0050789 name: regulation of biological process namespace: biological_process alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: goslim_generic subset: goslim_goa subset: gosubset_prok subset: PANTHERGOslim synonym: "regulation of physiological process" EXACT [] relationship: regulates GO:0008150 ! biological_process [Term] id: GO:0050828 name: regulation of liquid surface tension namespace: biological_process def: "Any process that modulates the surface tension of a liquid. Surface tension is the property that makes a liquid behave as if it had an elastic skin on its surface at the interface with a gas or an immiscible liquid." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: PANTHERGOslim synonym: "regulation of surface tension of a liquid" EXACT [] synonym: "surfactant activity" RELATED [] is_a: GO:0042592 ! homeostatic process [Term] id: GO:0050877 name: neurological system process namespace: biological_process def: "A organ system process carried out by any of the organs or tissues of neurological system." [GOC:ai, GOC:mtg_cardio] subset: goslim_pir subset: PANTHERGOslim synonym: "neurophysiological process" EXACT [] synonym: "pan-neural process" RELATED [] is_a: GO:0003008 ! system process [Term] id: GO:0050896 name: response to stimulus namespace: biological_process alt_id: GO:0051869 def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [GOC:ai] subset: goslim_goa subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "physiological response to stimulus" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0050909 name: sensory perception of taste namespace: biological_process def: "The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells." [GOC:ai, http://www.onelook.com/] subset: PANTHERGOslim synonym: "gustation" EXACT [] synonym: "sense of taste" EXACT [] synonym: "taste" EXACT [] synonym: "taste perception" EXACT [] is_a: GO:0007606 ! sensory perception of chemical stimulus [Term] id: GO:0051169 name: nuclear transport namespace: biological_process def: "The directed movement of substances into, out of, or within the nucleus." [GOC:ai] subset: PANTHERGOslim synonym: "nucleus transport" EXACT [] xref: Reactome:162590 is_a: GO:0006810 ! transport [Term] id: GO:0051179 name: localization namespace: biological_process def: "The processes by which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location." [GOC:ai] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "establishment and maintenance of cellular component location" NARROW [] synonym: "establishment and maintenance of localization" EXACT [] synonym: "establishment and maintenance of position" EXACT [] synonym: "establishment and maintenance of substance location" NARROW [] synonym: "establishment and maintenance of substrate location" NARROW [] is_a: GO:0008150 ! biological_process [Term] id: GO:0051180 name: vitamin transport namespace: biological_process def: "The directed movement of vitamins into, out of, within or between cells. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:ai] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "vitamin or cofactor transport" BROAD [] is_a: GO:0006810 ! transport [Term] id: GO:0051189 name: prosthetic group metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein." [GOC:ai] subset: goslim_pir subset: gosubset_prok subset: PANTHERGOslim synonym: "coenzyme and prosthetic group metabolic process" BROAD [] synonym: "coenzyme and prosthetic group metabolism" BROAD [] synonym: "prosthetic group metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0051726 name: regulation of cell cycle namespace: biological_process alt_id: GO:0000074 def: "Any process that modulates the rate or extent of progression through the cell cycle." [GOC:ai, GOC:dph, GOC:tb] subset: gosubset_prok subset: PANTHERGOslim synonym: "cell cycle control" EXACT [] synonym: "cell cycle modulation" EXACT [] synonym: "cell cycle regulation" EXACT [] synonym: "cell cycle regulator" RELATED [] synonym: "control of cell cycle progression" EXACT [] synonym: "modulation of cell cycle progression" EXACT [] synonym: "regulation of cell cycle progression" EXACT [] synonym: "regulation of progression through cell cycle" EXACT [] synonym: "tumor suppressor" RELATED [] xref: Reactome:156678 xref: Reactome:156699 xref: Reactome:156711 xref: Reactome:162657 xref: Reactome:204139 xref: Reactome:209045 xref: Reactome:209050 xref: Reactome:211608 xref: Reactome:213123 xref: Reactome:218715 xref: Reactome:218726 xref: Reactome:221382 xref: Reactome:222877 xref: Reactome:227596 xref: Reactome:230018 xref: Reactome:235842 xref: Reactome:235853 xref: Reactome:238231 xref: Reactome:239383 xref: Reactome:243028 xref: Reactome:243033 xref: Reactome:244651 xref: Reactome:245640 xref: Reactome:248176 xref: Reactome:248181 xref: Reactome:249585 xref: Reactome:250281 xref: Reactome:251600 xref: Reactome:252387 xref: Reactome:253031 xref: Reactome:254679 xref: Reactome:255542 xref: Reactome:256281 xref: Reactome:257921 xref: Reactome:258917 xref: Reactome:259656 xref: Reactome:261512 xref: Reactome:262291 xref: Reactome:264389 xref: Reactome:265239 xref: Reactome:267430 xref: Reactome:267435 xref: Reactome:268364 xref: Reactome:280849 xref: Reactome:282764 xref: Reactome:285431 xref: Reactome:285436 xref: Reactome:286566 relationship: regulates GO:0007049 ! cell cycle [Typedef] id: negatively_regulates name: negatively_regulates subset: PANTHERGOslim is_a: regulates ! regulates [Typedef] id: part_of name: part_of subset: PANTHERGOslim xref: OBO_REL:part_of is_transitive: true [Typedef] id: positively_regulates name: positively_regulates subset: PANTHERGOslim is_a: regulates ! regulates [Typedef] id: regulates name: regulates subset: PANTHERGOslim