Copyright (C) 2017 University of Southern California This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. ############################################################################ README for PANTHER Sequence Classifications http://www.pantherdb.org Last updated: Dec. 2018 ------------ The current version of the PANTHER HMM library is Version 130. The current Pathway release is version 3.6.2. The PANTHER website allows access to to pre-calculated HMM scoring results for the complete proteomes derived from the human, mouse, rat and Drosophila melanogaster genomes. A total of 131 classification files are provided here, one for each organism: PTHR14.0_Amborella PTHR14.0_aquifex PTHR14.0_arabidopsis PTHR14.0_ashbya PTHR14.0_aspergillus_fumigata PTHR14.0_aspergillus_nidulans PTHR14.0_bacillus_cereus PTHR14.0_bacillus_subtilis PTHR14.0_bacteroidetes PTHR14.0_banana PTHR14.0_barley PTHR14.0_barrel_medic PTHR14.0_bean PTHR14.0_black_cottonwood PTHR14.0_bradyrhizobium PTHR14.0_branchiostoma PTHR14.0_budding_yeast PTHR14.0_cabbage PTHR14.0_cacao PTHR14.0_candida PTHR14.0_cat PTHR14.0_c_briggsae PTHR14.0_chicken PTHR14.0_chimpanzee PTHR14.0_chlamydia PTHR14.0_chloroflexus PTHR14.0_cholera PTHR14.0_chytrid PTHR14.0_ciona PTHR14.0_clostridium PTHR14.0_cotton PTHR14.0_cow PTHR14.0_coxiella PTHR14.0_cryptococcus PTHR14.0_cucumber PTHR14.0_date_palm PTHR14.0_deinococcus PTHR14.0_dictyoglomus PTHR14.0_dictyostelium PTHR14.0_dog PTHR14.0_d_purpureum PTHR14.0_e_coli PTHR14.0_entamoeba PTHR14.0_fission_yeast PTHR14.0_frog PTHR14.0_fruit_fly PTHR14.0_fusobacterium PTHR14.0_geobacter PTHR14.0_giardia PTHR14.0_gloeobacter PTHR14.0_gorilla PTHR14.0_grape PTHR14.0_green_algae PTHR14.0_halobacterium PTHR14.0_helobdella PTHR14.0_h_flu PTHR14.0_horse PTHR14.0_h_pylori PTHR14.0_human PTHR14.0_korarchaeum PTHR14.0_leishmania PTHR14.0_lepisosteudae PTHR14.0_leptospira PTHR14.0_listeria PTHR14.0_lizard PTHR14.0_macacque PTHR14.0_maize PTHR14.0_meningococcus PTHR14.0_methanocaldococcus PTHR14.0_methanosarcina PTHR14.0_m_genitalium PTHR14.0_millet PTHR14.0_monosiga PTHR14.0_mosquito PTHR14.0_moss PTHR14.0_mouse PTHR14.0_mycobacterium PTHR14.0_nematode_worm PTHR14.0_nematostella PTHR14.0_neurospora PTHR14.0_nitrosopumilu PTHR14.0_opossum PTHR14.0_orange PTHR14.0_oryzias PTHR14.0_Ostreococcus PTHR14.0_paramecium PTHR14.0_peach PTHR14.0_phaeosphaeria PTHR14.0_phytophthora PTHR14.0_pig PTHR14.0_plasmodium PTHR14.0_platypus PTHR14.0_pristionchus PTHR14.0_pseudomonas PTHR14.0_puccinia PTHR14.0_purple_false_brome PTHR14.0_pyrobaculum PTHR14.0_rat PTHR14.0_rhodopirellula PTHR14.0_rice PTHR14.0_salmonella PTHR14.0_sclerotinia PTHR14.0_sea_urchin PTHR14.0_shewanella PTHR14.0_sorghum PTHR14.0_soybean PTHR14.0_staph PTHR14.0_strep PTHR14.0_streptomyces PTHR14.0_sulfolobus PTHR14.0_sunflower PTHR14.0_synechocystis PTHR14.0_t_brucei PTHR14.0_thalassiosira PTHR14.0_thermococcus PTHR14.0_thermodesulfovibrio PTHR14.0_thermotoga PTHR14.0_tick PTHR14.0_tobacco PTHR14.0_tomato PTHR14.0_tribolium PTHR14.0_trichomonas PTHR14.0_trichoplax PTHR14.0_ustilago PTHR14.0_water_flea PTHR14.0_wheat PTHR14.0_xanthomonas PTHR14.0_yarrowia PTHR14.0_yellow_monkey flower PTHR14.0_yersinia PTHR14.0_zebrafish Assigning classifications to genes The assignment is based on the phylogenetic trees where the gene is located. The annotation of the subfamilies are used for the gene. Format of tab-delimited classification file: 1) Gene Identifier (format: organism|gene id source:gene id|protein id source:protein id) Example: XENTR|ENSEMBL:ENSXETG00000001299|ENSEMBL:ENSXETP00000002787 HUMAN|ENSEMBL:ENSG00000197601|UniProtKB:Q8WVX9 2) Protein ID - currently empty. The protein ids can be retrieved from above 3) PANTHER SF ID – for example, PTHR12213:SF6. ":SF" indicates the subfamily ID 4) PANTHER Family Name 5) PANTHER Subfamily Name 6) PANTHER Molecular function 7) PANTHER Biological process 8) Cellular components: PANTHER GO slim cellular component terms assigned to families and subfamilies 9) Protein class: PANTHER protein class terms assigned to families and subfamilies 10) Pathway Example Molecular function (the same format applies to biological process, cellular component and protein class) transferase activity#GO:0016740;enzyme regulator activity#GO:0030234;protein binding#GO:0005515 Example Pathway: Inflammation mediated by chemokine and cytokine signaling pathway#Inflammation mediated by chemokine and cytokine signaling pathway#P00031>Integrin#Integrin#P00853;Integrin signalling pathway#Integrin signalling pathway#P00034>Integrin alpha#Integrin alpha#P00941 The format of the pathway information is: pathway_long_name#pathway_short_name#pathway_accession>component_long_name#component_short_name#component_accession Explanation of pathway accessions: Gxxxxx Gene or RNA Pxxxxx Protein Sxxxxx small molecules Uxxxxx others, such as "unknown", etc. ----- If you have any questions, please contact us at: feedback@pantherdb.org ----- Version History December 19, 2018 - PANTHER 14.0 and Pathway 3.6.2 October 24, 2017 - PANTHER 13.0 and Pathway 3.6 January 24, 2014 - PANTHER 9.0 and Pathway 3.3 February 22, 2008 - PANTHER Pathway 2.1 January 27, 2007 - Entrez Gene and RefSeq Data updated May 20, 2010 - PANTHER7.0 December 8, 2006 - PANTHER6.1 September 29, 2006 - update to fix bug where some subfamilies had tabs in the subfamily name July 20, 2006 - update for PANTHER Pathway Version 1.3. Also, there was missing data in the original release, and this has now been fixed February 16, 2006 - original release