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Version Information

This page presents a partial list of the data sources we download and integrate in our database. These data sources are created and maintained by groups other than ourselves, and we wish to thank these other groups for so generously providing their data to us and the rest of the scientific community.
The first section shows "datasets". Each dataset generally consist of many files which are released as a unit. The table shows the name of each dataset which is linked to the dataset's homepage, and the name or date of the release used in the current version of our database. In a few cases, no release name or date was available.
The second section shows the individual files that we download. The table indicates the full URL of each file, the date the file was updated by its maintainer, and the date we downloaded it. Note that the URL of the file is not hyperlinked, since clicking on such a link would cause the file to be downloaded to your computer which is probably not desirable. We have not grouped the files by data source since this is usually apparent from the URL.
The list of sources presented here is incomplete. Additional sources will be added in future releases.

Dataset Release
BioCarta (linked to genes using data from NCI Cancer Gene Anatomy Project) information not available
Bioconductor Microarray Annotation Version 2.4.1, 23-Apr-2010
BioGRID Version 3.0.68, 25-Aug-2010
Database of Interacting Proteins (DIP) 14-Jun-2010
DoTS (Database Of Transcribed Sequences) human Release 10, 21-Apr-2008
mouse Release 11, 21-Apr-2008
Ensembl Release 59, Aug-2010
Gene Ontology Consortium Version 1.1466, 28-Sep-2010
Genetic Association Database 01-Oct-2007
HUGO Gene Nomenclature Committee information not available
Human Protein Reference Database (HPRD) Release 9, 13-Apr-2010
InParanoid: Eukaryotic Ortholog Groups Version 7.0, 28-Jun-2009
IntAct 03-Sep-2010
IPI (International Protein Index) Version 3.75, 19-Aug-2010
KEGG: Kyoto Encyclopedia of Genes and Genomes Release 55.1, 01-Sep-2010
MINT: a Molecular INTeraction database BINARY 2.6, 28-Jul-2010
Mouse Genome Informatics (MGI), Jackson Laboratory 29-Sep-2010
NCBI Entrez Gene 29-Sep-2010
NCBI HomoloGene Release 64, 08-Aug-2009
NCBI UniGene human Build #226, 05-Aug-2010
mouse Build #186, 24-Jul-2010
rat Build #186, 30-Aug-2010
OMIM, Online Mendelian Inheritance in Man information not available
OrthoMCL Version 2.0, 06-Dec-2009
PeptideAtlas May-2010
Rat Genome Database 21-Sep-2010
Reactome - a curated knowledgebase of biological pathways Version 33, 18-Jun-2010
Sanger Interaction Map 13-Aug-2004
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) Version 8.3
The MIPS Mammalian Protein-Protein Interaction Database information not available
UCSC Genome Bioinformatics (Golden Path) human UCSC hg19, NCBI build CRCh37, Feb-2009
mouse UCSC mm9, NCBI Build 37.1, July-2007
rat UCSC rn4, RGSC version 3.4, Nov-2004
UniProt (Universal Protein Resource) Release 2010_09, 10-Aug-2010

File Update Date Download Date
ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip 08-Sep-2010 29-Sep-2010
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.dat.gz 19-Aug-2010 29-Sep-2010
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.MOUSE.dat.gz 19-Aug-2010 29-Sep-2010
ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.RAT.dat.gz 19-Aug-2010 29-Sep-2010
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/hsapiens_gene_ensembl__homolog_Mmus__dm.txt.gz 01-May-2009 29-Sep-2010
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/hsapiens_gene_ensembl__homolog_Rnor__dm.txt.gz 01-May-2009 29-Sep-2010
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/mmusculus_gene_ensembl__homolog_Hsap__dm.txt.gz 01-May-2009 29-Sep-2010
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/mmusculus_gene_ensembl__homolog_Rnor__dm.txt.gz 01-May-2009 29-Sep-2010
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/rnorvegicus_gene_ensembl__homolog_Hsap__dm.txt.gz 01-May-2009 29-Sep-2010
ftp://ftp.ensembl.org/pub/release-54/mysql/ensembl_mart_54/rnorvegicus_gene_ensembl__homolog_Mmus__dm.txt.gz 01-May-2009 29-Sep-2010
ftp://ftp.expasy.org/databases/enzyme/enzyme.dat 10-Sep-2010 29-Sep-2010
ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology.obo 29-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/ko 29-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ko.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_ncbi-geneid.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/hsa/hsa_pathway.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ko.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_ncbi-geneid.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/mmu/mmu_pathway.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ko.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_ncbi-geneid.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/genes/organisms/rno/rno_pathway.list 28-Sep-2010 30-Sep-2010
ftp://ftp.genome.ad.jp/pub/kegg/pathway/map_title.tab 28-Sep-2010 29-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human1.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human2.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human3.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Human4.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat1.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat2.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat3.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_Rat4.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman1.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman2.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman3.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/HMD_RatHuman4.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.informatics.jax.org/pub/reports/MGI_EntrezGene.rpt 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2unigene 29-Sep-2010 29-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/gene/DATA/README 15-Sep-2010 29-Sep-2010
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build63/homologene.data 08-Jan-2009 29-Sep-2010
ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z 29-Sep-2010 30-Sep-2010
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz 08-Sep-2010 29-Sep-2010
ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.retired.lst.gz 08-Sep-2010 29-Sep-2010
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz 18-Aug-2010 29-Sep-2010
ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.retired.lst.gz 18-Aug-2010 29-Sep-2010
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.data.gz 20-Sep-2010 29-Sep-2010
ftp://ftp.ncbi.nih.gov/repository/UniGene/Rattus_norvegicus/Rn.retired.lst.gz 20-Sep-2010 29-Sep-2010
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human 02-Sep-2009 29-Sep-2010
ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse 28-Nov-2007 29-Sep-2010
ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/HGNC_gene_lists290910.tsv 29-Sep-2010 30-Sep-2010
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/complete.txt.gz 26-Apr-2004 29-Sep-2010
ftp://ftp.sanger.ac.uk/pub/postgenomics/signaltransduction/interactionmap/core.txt.gz 26-Apr-2004 29-Sep-2010
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz 10-Aug-2010 29-Sep-2010
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.dat.gz 10-Aug-2010 29-Sep-2010
ftp://ftp1.nci.nih.gov/pub/CGAP/Hs_GeneData.dat 15-Sep-2010 29-Sep-2010
ftp://ftp1.nci.nih.gov/pub/CGAP/Mm_GeneData.dat 24-Aug-2010 29-Sep-2010
ftp://ftp1.nci.nih.gov/pub/PID/uniprot/uniprot.tab.gz 17-Sep-2010 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/chromInfo.txt.gz 27-Apr-2009 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/cytoBand.txt.gz 14-Jun-2009 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens/database/knownToLocusLink.txt.gz 06-Dec-2009 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/chromInfo.txt.gz 22-Aug-2007 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/cytoBand.txt.gz 22-Aug-2007 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/knownToLocusLink.txt.gz 12-Oct-2007 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/chromInfo.txt.gz 20-Jun-2006 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/cytoBand.txt.gz 20-Jun-2006 29-Sep-2010
ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Rattus_norvegicus/database/knownToLocusLink.txt.gz 20-Jun-2006 29-Sep-2010
ftp://mint.bio.uniroma2.it/pub/release/mitab26/current/2010-07-27-mint-Mammalia-binary.mitab26.txt 28-Jul-2010 29-Sep-2010
ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN 20-Sep-2010 29-Sep-2010
ftp://rgd.mcw.edu/pub/data_release/GENES_MOUSE 20-Sep-2010 29-Sep-2010
ftp://rgd.mcw.edu/pub/data_release/GENES_RAT 20-Sep-2010 29-Sep-2010
ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS 21-Sep-2010 29-Sep-2010
http://banon.cshl.edu:5555/biomart/martservice 30-Sep-2010
http://geneticassociationdb.nih.gov/all.xls 06-Jul-2006 30-Sep-2010
http://inparanoid.sbc.su.se/download/7.0_current/table_stats/InParanoid.H.sapiens-M.musculus 28-Apr-2009 30-Sep-2010
http://inparanoid.sbc.su.se/download/7.0_current/table_stats/InParanoid.H.sapiens-R.norvegicus 28-Apr-2009 30-Sep-2010
http://inparanoid.sbc.su.se/download/7.0_current/table_stats/InParanoid.M.musculus-R.norvegicus 28-Apr-2009 30-Sep-2010
http://mips.gsf.de/proj/ppi/data/mppi.gz 01-Jun-2004 30-Sep-2010
http://plugins.gnf.org/download/gnf1h-anntable.zip 19-Nov-2009 30-Sep-2010
http://plugins.gnf.org/download/gnf1h-gcrma.zip 03-Feb-2010 29-Sep-2010
http://string.embl.de/newstring_download/protein.links.detailed.v8.3.txt.gz 25-Jun-2010 30-Sep-2010
http://string.embl.de/newstring_download/protein.links.v8.3.txt.gz 25-Jun-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu133a.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu133a2.db_2.4.1.tar.gz 30-Mar-2010 29-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu133b.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu133plus2.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu95a.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu95av2.db_2.4.1.tar.gz 30-Mar-2010 29-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu95b.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu95c.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu95d.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/hgu95e.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/lumiHumanIDMapping_1.6.2.tar.gz 10-May-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/lumiMouseIDMapping_1.6.2.tar.gz 10-May-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/lumiRatIDMapping_1.6.2.tar.gz 10-May-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/mgu74a.db_2.4.1.tar.gz 30-Mar-2010 29-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/mgu74av2.db_2.4.1.tar.gz 30-Mar-2010 29-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/mouse4302.db_2.4.1.tar.gz 30-Mar-2010 29-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/rae230a.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/rat2302.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.bioconductor.org/packages/release/data/annotation/src/contrib/rgu34a.db_2.4.1.tar.gz 30-Mar-2010 30-Sep-2010
http://www.cbil.upenn.edu/downloads/DoTS/current_human/humDoTS_DTToGeneId.dat.gz 10-Mar-2008 30-Sep-2010
http://www.cbil.upenn.edu/downloads/DoTS/current_mouse/musDoTS_DTToGeneId.dat.gz 06-Apr-2007 29-Sep-2010
http://www.genenames.org/cgi-bin/hgnc_downloads.cgi 30-Sep-2010
http://www.orthomcl.org/common/downloads/release-4/groups_OrthoMCL-4.txt.gz 06-Dec-2009 30-Sep-2010
http://www.peptideatlas.org/builds/human/HumanP0.9/200704/APD_ensembl_hits.tsv 13-Apr-2007 29-Sep-2010
http://www.peptideatlas.org/builds/human/plasma/data/2007_04/PA_HsP_2007-04_Ens43_P0.9_pep2prot.tsv 13-Apr-2007 30-Sep-2010
http://www.reactome.org/download/current/homo_sapiens.interactions.txt.gz 11-Jun-2010 29-Sep-2010