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: Oct. 2017
------------

The current version of the PANTHER HMM library is Version 130.  The current Pathway release is version 3.6.

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

PTHR13.0_aquifex
PTHR13.0_arabidopsis
PTHR13.0_ashbya
PTHR13.0_aspergillus_fumigata
PTHR13.0_aspergillus_nidulans
PTHR13.0_bacillus_cereus
PTHR13.0_bacillus_subtilis
PTHR13.0_bacteroidetes
PTHR13.0_black_cottonwood
PTHR13.0_bradyrhizobium
PTHR13.0_branchiostoma
PTHR13.0_budding_yeast
PTHR13.0_candida
PTHR13.0_cat
PTHR13.0_c_briggsae
PTHR13.0_chicken
PTHR13.0_chimpanzee
PTHR13.0_chlamydia
PTHR13.0_chloroflexus
PTHR13.0_cholera
PTHR13.0_chytrid
PTHR13.0_ciona
PTHR13.0_clostridium
PTHR13.0_cow
PTHR13.0_coxiella
PTHR13.0_cryptococcus
PTHR13.0_deinococcus
PTHR13.0_dictyoglomus
PTHR13.0_dictyostelium
PTHR13.0_dog
PTHR13.0_d_purpureum
PTHR13.0_e_coli
PTHR13.0_entamoeba
PTHR13.0_fission_yeast
PTHR13.0_frog
PTHR13.0_fruit_fly
PTHR13.0_fusobacterium
PTHR13.0_geobacter
PTHR13.0_giardia
PTHR13.0_gloeobacter
PTHR13.0_gorilla
PTHR13.0_grape
PTHR13.0_green_algae
PTHR13.0_halobacterium
PTHR13.0_helobdella
PTHR13.0_h_flu
PTHR13.0_horse
PTHR13.0_h_pylori
PTHR13.0_human
PTHR13.0_korarchaeum
PTHR13.0_leishmania
PTHR13.0_lepisosteudae
PTHR13.0_leptospira
PTHR13.0_listeria
PTHR13.0_lizard
PTHR13.0_macacque
PTHR13.0_maize
PTHR13.0_meningococcus
PTHR13.0_methanocaldococcus
PTHR13.0_methanosarcina
PTHR13.0_m_genitalium
PTHR13.0_monosiga
PTHR13.0_mosquito
PTHR13.0_moss
PTHR13.0_mouse
PTHR13.0_mycobacterium
PTHR13.0_nematode_worm
PTHR13.0_nematostella
PTHR13.0_neurospora
PTHR13.0_nitrosopumilu
PTHR13.0_opossum
PTHR13.0_oryzias
PTHR13.0_paramecium
PTHR13.0_phaeosphaeria
PTHR13.0_phytophthora
PTHR13.0_pig
PTHR13.0_plasmodium
PTHR13.0_platypus
PTHR13.0_pristionchus
PTHR13.0_pseudomonas
PTHR13.0_puccinia
PTHR13.0_purple_false_brome
PTHR13.0_pyrobaculum
PTHR13.0_rat
PTHR13.0_rhodopirellula
PTHR13.0_rice
PTHR13.0_salmonella
PTHR13.0_sclerotinia
PTHR13.0_sea_urchin
PTHR13.0_shewanella
PTHR13.0_soybean
PTHR13.0_staph
PTHR13.0_strep
PTHR13.0_streptomyces
PTHR13.0_sulfolobus
PTHR13.0_synechocystis
PTHR13.0_t_brucei
PTHR13.0_thalassiosira
PTHR13.0_thermococcus
PTHR13.0_thermodesulfovibrio
PTHR13.0_thermotoga
PTHR13.0_tick
PTHR13.0_tomato
PTHR13.0_tribolium
PTHR13.0_trichomonas
PTHR13.0_trichoplax
PTHR13.0_ustilago
PTHR13.0_water_flea
PTHR13.0_xanthomonas
PTHR13.0_yarrowia
PTHR13.0_yersinia
PTHR13.0_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

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