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README for PANTHER Sequence Classifications
http://www.pantherdb.org
Last updated: December 2020
------------

The current version of the PANTHER HMM library is Version 131.  The current Pathway release is version 3.6.5.

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

PTHR15.0_Amborella
PTHR15.0_aquifex
PTHR15.0_arabidopsis
PTHR15.0_ashbya
PTHR15.0_aspergillus_fumigata
PTHR15.0_aspergillus_nidulans
PTHR15.0_bacillus_cereus
PTHR15.0_bacillus_subtilis
PTHR15.0_bacteroidetes
PTHR15.0_banana
PTHR15.0_barley
PTHR15.0_barrel_medic
PTHR15.0_bean
PTHR15.0_bell_pepper
PTHR15.0_black_cottonwood
PTHR15.0_bradyrhizobium
PTHR15.0_branchiostoma
PTHR15.0_budding_yeast
PTHR15.0_cabbage
PTHR15.0_cacao
PTHR15.0_candida
PTHR15.0_cassava
PTHR15.0_cat
PTHR15.0_c_briggsae
PTHR15.0_chicken
PTHR15.0_chimpanzee
PTHR15.0_chlamydia
PTHR15.0_chloroflexus
PTHR15.0_cholera
PTHR15.0_chytrid
PTHR15.0_ciona
PTHR15.0_clostridium
PTHR15.0_cotton
PTHR15.0_cow
PTHR15.0_coxiella
PTHR15.0_cryptococcus
PTHR15.0_cucumber
PTHR15.0_date_palm
PTHR15.0_deinococcus
PTHR15.0_dictyoglomus
PTHR15.0_dictyostelium
PTHR15.0_dog
PTHR15.0_d_purpureum
PTHR15.0_e_coli
PTHR15.0_eelgrass
PTHR15.0_english_walnut
PTHR15.0_entamoeba
PTHR15.0_fission_yeast
PTHR15.0_flooded_gum
PTHR15.0_frog
PTHR15.0_fruit_fly
PTHR15.0_fusobacterium
PTHR15.0_garden_lettuce
PTHR15.0_geobacter
PTHR15.0_giardia
PTHR15.0_gloeobacter
PTHR15.0_gorilla
PTHR15.0_grape
PTHR15.0_green_algae
PTHR15.0_halobacterium
PTHR15.0_helobdella
PTHR15.0_h_flu
PTHR15.0_horse
PTHR15.0_h_pylori
PTHR15.0_human
PTHR15.0_korarchaeum
PTHR15.0_leishmania
PTHR15.0_lepisosteudae
PTHR15.0_leptospira
PTHR15.0_listeria
PTHR15.0_lizard
PTHR15.0_macacque
PTHR15.0_maize
PTHR15.0_meningococcus
PTHR15.0_methanocaldococcus
PTHR15.0_methanosarcina
PTHR15.0_m_genitalium
PTHR15.0_millet
PTHR15.0_monosiga
PTHR15.0_mosquito
PTHR15.0_moss
PTHR15.0_mouse
PTHR15.0_mycobacterium
PTHR15.0_nematode_worm
PTHR15.0_nematostella
PTHR15.0_neurospora
PTHR15.0_nitrosopumilu
PTHR15.0_opossum
PTHR15.0_orange
PTHR15.0_oryzias
PTHR15.0_Ostreococcus
PTHR15.0_paramecium
PTHR15.0_peach
PTHR15.0_phaeosphaeria
PTHR15.0_phytophthora
PTHR15.0_pig
PTHR15.0_plasmodium
PTHR15.0_platypus
PTHR15.0_potato
PTHR15.0_pristionchus
PTHR15.0_pseudomonas
PTHR15.0_puccinia
PTHR15.0_purple_false_brome
PTHR15.0_pyrobaculum
PTHR15.0_rape
PTHR15.0_rat
PTHR15.0_rhodopirellula
PTHR15.0_rice
PTHR15.0_sacred_lotus
PTHR15.0_salmonella
PTHR15.0_sclerotinia
PTHR15.0_sea_urchin
PTHR15.0_shewanella
PTHR15.0_sorghum
PTHR15.0_soybean
PTHR15.0_spikemoss
PTHR15.0_spinach
PTHR15.0_staph
PTHR15.0_strep
PTHR15.0_streptomyces
PTHR15.0_sulfolobus
PTHR15.0_sunflower
PTHR15.0_synechocystis
PTHR15.0_t_brucei
PTHR15.0_thalassiosira
PTHR15.0_thermococcus
PTHR15.0_thermodesulfovibrio
PTHR15.0_thermotoga
PTHR15.0_tick
PTHR15.0_tobacco
PTHR15.0_tomato
PTHR15.0_tribolium
PTHR15.0_trichomonas
PTHR15.0_trichoplax
PTHR15.0_ustilago
PTHR15.0_water_flea
PTHR15.0_wheat
PTHR15.0_xanthomonas
PTHR15.0_yarrowia
PTHR15.0_yellow_monkey_flower
PTHR15.0_yersinia
PTHR15.0_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

December 18, 2020 - PANTHER 16.0 and Pathway 3.6.5
February 14, 2020 - PANTHER 15.0 and Pathway 3.6.4
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