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README for PANTHER Sequence Classifications
http://www.pantherdb.org
Last updated: March 2019
------------

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

PTHR14.1_Amborella_
PTHR14.1_aquifex_
PTHR14.1_arabidopsis_
PTHR14.1_ashbya_
PTHR14.1_aspergillus_fumigata
PTHR14.1_aspergillus_nidulans
PTHR14.1_bacillus_cereus_
PTHR14.1_bacillus_subtilis_
PTHR14.1_bacteroidetes_
PTHR14.1_banana_
PTHR14.1_barley_
PTHR14.1_barrel_medic
PTHR14.1_bean_
PTHR14.1_black_cottonwood_
PTHR14.1_bradyrhizobium_
PTHR14.1_branchiostoma_
PTHR14.1_budding_yeast_
PTHR14.1_cabbage_
PTHR14.1_cacao_
PTHR14.1_candida_
PTHR14.1_cat_
PTHR14.1_c_briggsae_
PTHR14.1_chicken_
PTHR14.1_chimpanzee_
PTHR14.1_chlamydia_
PTHR14.1_chloroflexus_
PTHR14.1_cholera_
PTHR14.1_chytrid_
PTHR14.1_ciona_
PTHR14.1_clostridium_
PTHR14.1_cotton_
PTHR14.1_cow_
PTHR14.1_coxiella_
PTHR14.1_cryptococcus_
PTHR14.1_cucumber_
PTHR14.1_date_palm
PTHR14.1_deinococcus_
PTHR14.1_dictyoglomus_
PTHR14.1_dictyostelium_
PTHR14.1_dog_
PTHR14.1_d_purpureum_
PTHR14.1_e_coli_
PTHR14.1_eelgrass_
PTHR14.1_entamoeba_
PTHR14.1_fission_yeast_
PTHR14.1_frog_
PTHR14.1_fruit_fly_
PTHR14.1_fusobacterium_
PTHR14.1_geobacter_
PTHR14.1_giardia_
PTHR14.1_gloeobacter_
PTHR14.1_gorilla_
PTHR14.1_grape_
PTHR14.1_green_algae_
PTHR14.1_halobacterium_
PTHR14.1_helobdella_
PTHR14.1_h_flu_
PTHR14.1_horse_
PTHR14.1_h_pylori_
PTHR14.1_human_
PTHR14.1_korarchaeum_
PTHR14.1_leishmania_
PTHR14.1_lepisosteudae_
PTHR14.1_leptospira_
PTHR14.1_listeria_
PTHR14.1_lizard_
PTHR14.1_macacque_
PTHR14.1_maize_
PTHR14.1_meningococcus_
PTHR14.1_methanocaldococcus_
PTHR14.1_methanosarcina_
PTHR14.1_m_genitalium_
PTHR14.1_millet_
PTHR14.1_monosiga_
PTHR14.1_mosquito_
PTHR14.1_moss_
PTHR14.1_mouse_
PTHR14.1_mycobacterium_
PTHR14.1_nematode_worm_
PTHR14.1_nematostella_
PTHR14.1_neurospora_
PTHR14.1_nitrosopumilu_
PTHR14.1_opossum_
PTHR14.1_orange_
PTHR14.1_oryzias_
PTHR14.1_Ostreococcus_
PTHR14.1_paramecium_
PTHR14.1_peach_
PTHR14.1_phaeosphaeria_
PTHR14.1_phytophthora_
PTHR14.1_pig_
PTHR14.1_plasmodium_
PTHR14.1_platypus_
PTHR14.1_pristionchus_
PTHR14.1_pseudomonas_
PTHR14.1_puccinia_
PTHR14.1_purple_false_brome_
PTHR14.1_pyrobaculum_
PTHR14.1_rat_
PTHR14.1_rhodopirellula_
PTHR14.1_rice_
PTHR14.1_salmonella_
PTHR14.1_sclerotinia_
PTHR14.1_sea_urchin_
PTHR14.1_shewanella_
PTHR14.1_sorghum_
PTHR14.1_soybean_
PTHR14.1_staph_
PTHR14.1_strep_
PTHR14.1_streptomyces_
PTHR14.1_sulfolobus_
PTHR14.1_sunflower_
PTHR14.1_synechocystis_
PTHR14.1_t_brucei_
PTHR14.1_thalassiosira_
PTHR14.1_thermococcus_
PTHR14.1_thermodesulfovibrio_
PTHR14.1_thermotoga_
PTHR14.1_tick_
PTHR14.1_tobacco_
PTHR14.1_tomato_
PTHR14.1_tribolium_
PTHR14.1_trichomonas_
PTHR14.1_trichoplax_
PTHR14.1_ustilago_
PTHR14.1_water_flea_
PTHR14.1_wheat_
PTHR14.1_xanthomonas_
PTHR14.1_yarrowia_
PTHR14.1_yellow_monkey flower
PTHR14.1_yersinia_
PTHR14.1_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

March 20, 2019 - PANTHER 14.1 and Pathway 3.6.2
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