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| == 16-12-2010 Release GO-Pathways-PFAM == === Sources === * Gene-Ontology BP, CC, MF (up-propagated, all evidence codes) * KEGG Pathways * NCI Pathways * Biocarta Pathways * PFAM Protein Domains === R Code and Release Notes === R code to format the gene-sets * [[attachment:GeneSet_DB_v02_exec20101108.R|R Code]] === Gene-sets (GMT format) === GMT is the standard gene-set format adopted by a few resources, such as GSEA. Original [[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29|description page]] * [[attachment:GO_K_NCI_BIOC_PF_Hs_eg.GMT|Human]] * [[attachment:GO_K_NCI_BIOC_PF_Mm_eg.GMT|Mouse]] * [[attachment:GO_K_NCI_BIOC_PF_Rn_eg.GMT|Rat]] {{{ RELEASE INFO |
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| == Code == | org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db (GO, KEGG gene-set ID to gene ID) - Package version: 2.4.6 - R version: 2.12.0 - Packaged: 2010-10-04 - Built: 2010-10-21 |
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| == 20010 09 10 Release == | GO.db (GO gene-set ID to name) - Package version: 2.4.5 - R version: 2.12.0 - Packaged: 2010-09-23 - Built: 2010-10-21 KEGG.db (KEGG pathway ID to name) - Package version: 2.4.5 - R version: 2.12.0 - Packaged: 2010-09-23 - Built: 2010-10-21 NCI - annotations downloaded from website (Uniprot ID, human): 2010-11-08 BioCarta - annotations downloaded from WhichGenes (Entrez-Gene ID, human): 2010-03-26 PFAM ... }}} === Orthology Table === * [[attachment:Homologene_Build65_20100910.txt|NCBI Homologene Build 65]] == Questions? == * email: daniele [dot] merico [atsign] gmail [dot] com |
Gene-set Collections
16-12-2010 Release GO-Pathways-PFAM
Sources
- Gene-Ontology BP, CC, MF (up-propagated, all evidence codes)
- KEGG Pathways
- NCI Pathways
- Biocarta Pathways
- PFAM Protein Domains
R Code and Release Notes
R code to format the gene-sets
Gene-sets (GMT format)
GMT is the standard gene-set format adopted by a few resources, such as GSEA. Original description page
RELEASE INFO org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db (GO, KEGG gene-set ID to gene ID) - Package version: 2.4.6 - R version: 2.12.0 - Packaged: 2010-10-04 - Built: 2010-10-21 GO.db (GO gene-set ID to name) - Package version: 2.4.5 - R version: 2.12.0 - Packaged: 2010-09-23 - Built: 2010-10-21 KEGG.db (KEGG pathway ID to name) - Package version: 2.4.5 - R version: 2.12.0 - Packaged: 2010-09-23 - Built: 2010-10-21 NCI - annotations downloaded from website (Uniprot ID, human): 2010-11-08 BioCarta - annotations downloaded from WhichGenes (Entrez-Gene ID, human): 2010-03-26 PFAM ...
Orthology Table
Questions?
- email: daniele [dot] merico [atsign] gmail [dot] com