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README for PANTHER Sequence Classifications
http://www.pantherdb.org
Last updated: Jun. 2016
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The current version of the PANTHER HMM library is Version 11.0.  The current Pathway release is version 3.4.1.

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 104 classification files are provided here, one for each organism:

PTHR11.0_aquifex
PTHR11.0_arabidopsis
PTHR11.0_ashbya
PTHR11.0_aspergillus
PTHR11.0_bacillus_cereus
PTHR11.0_bacillus_subtilis
PTHR11.0_bacteroidetes
PTHR11.0_black_cottonwood
PTHR11.0_bradyrhizobium
PTHR11.0_branchiostoma
PTHR11.0_budding_yeast
PTHR11.0_candida
PTHR11.0_cat
PTHR11.0_c_briggsae
PTHR11.0_chicken
PTHR11.0_chimpanzee
PTHR11.0_chlamydia
PTHR11.0_chloroflexus
PTHR11.0_cholera
PTHR11.0_chytrid
PTHR11.0_ciona
PTHR11.0_clostridium
PTHR11.0_cow
PTHR11.0_coxiella
PTHR11.0_cryptococcus
PTHR11.0_deinococcus
PTHR11.0_dictyoglomus
PTHR11.0_dictyostelium
PTHR11.0_dog
PTHR11.0_d_purpureum
PTHR11.0_e_coli
PTHR11.0_entamoeba
PTHR11.0_fission_yeast
PTHR11.0_frog
PTHR11.0_fruit_fly
PTHR11.0_fugu
PTHR11.0_fusobacterium
PTHR11.0_geobacter
PTHR11.0_giardia
PTHR11.0_gloeobacter
PTHR11.0_grape
PTHR11.0_green_algae
PTHR11.0_halobacterium
PTHR11.0_h_flu
PTHR11.0_horse
PTHR11.0_human
PTHR11.0_korarchaeum
PTHR11.0_leishmania
PTHR11.0_leptospira
PTHR11.0_listeria
PTHR11.0_lizard
PTHR11.0_macacque
PTHR11.0_methanocaldococcus
PTHR11.0_methanosarcina
PTHR11.0_monosiga
PTHR11.0_mosquito
PTHR11.0_moss
PTHR11.0_mouse
PTHR11.0_mycobacterium
PTHR11.0_nematode_worm
PTHR11.0_nematostella
PTHR11.0_neurospora
PTHR11.0_opossum
PTHR11.0_phaeosphaeria
PTHR11.0_phytophthora
PTHR11.0_pig
PTHR11.0_plasmodium
PTHR11.0_platypus
PTHR11.0_pristionchus
PTHR11.0_pseudomonas
PTHR11.0_puccinia
PTHR11.0_purple_false_brome
PTHR11.0_pyrobaculum
PTHR11.0_pyrococcus
PTHR11.0_rat
PTHR11.0_rhodopirellula
PTHR11.0_rice
PTHR11.0_salmonella
PTHR11.0_schistosoma
PTHR11.0_sclerotinia
PTHR11.0_sea_urchin
PTHR11.0_shewanella
PTHR11.0_sorghum
PTHR11.0_soybean
PTHR11.0_staph
PTHR11.0_strep
PTHR11.0_streptomyces
PTHR11.0_sulfolobus
PTHR11.0_synechocystis
PTHR11.0_t_brucei
PTHR11.0_tetrahymena
PTHR11.0_thalassiosira
PTHR11.0_thermodesulfovibrio
PTHR11.0_thermotoga
PTHR11.0_tick
PTHR11.0_tomato
PTHR11.0_trichomonas
PTHR11.0_trichoplax
PTHR11.0_ustilago
PTHR11.0_water_flea
PTHR11.0_xanthomonas
PTHR11.0_yarrowia
PTHR11.0_yersinia
PTHR11.0_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.

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If you have any questions, please contact us at: feedback@pantherdb.org
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Version History

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