Geneset Collections

MSigDB Genesets:

The MSigDB Geneset collections in their v2.5 Release (April 2008) have been downloaded from
[3] in the GMT format (cX.YYY.v2.5.symbols.gmt)

Links:

Following collections were used:

MSigDB.c2: file: c2.all.v2.5.symbols.gmt; 1892 curated genesets,
consists of 639 canonical pathways (cp), 1168 chemical and genetic perturbations (cgp) and 67 other genesets.
MSigDB.c2.cp: file: c2.cp.v2.5.symbols.gmt; 639 canonical pathways
(subset of MSigDB.c2.all)
MSigDB.c3: file: c3.all.v2.5.symbols.gmt
837 motif gene sets
consists of 222 microRNA target gene sets (mir), 500 transcription factor target gene sets (tft) and 115 other gene sets
MSigDB.c3.tft: file: c3.tft.v2.5.symbols.gmt
500 transcription factor targets
(subset of MSigDB.c3.all)
MSigDB.c5: file: c5.all.v2.5.symbols.gmt
1454 Gene Ontology gene sets,
consists of 233 GO cellular components (cc), 825 GO biological processes (bp) and 396 GO molecular functions (mf)

Pathway Gene Sets

file: pathways.all.2010_02.hs.symbols.gmt
This collection of Pathway gene sets was assembled in-house with data from the following resources:

Biocarta (http://www.biocarta.com/)
Cancer Cell Map(http://cancer.cellmap.org/)
HumanCyc (http://humancyc.org/)
INOH (http://www.inoh.org)
NCI (http://pid.nci.nih.gov/)
Netpath (http://www.netpath.org/)
Reactome (http://www.reactome.org/)

The gene-IDs from the original resources have been converted from RefSeq (or in case of Reactome from Uniprot) to Human Entrez-Gene ID's and further to human gene symbols using tranlation tables aquired from Biomart.
Analog to Chapter 2.2 to: Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, et al. (2010) Pathway Analysis of Dilated Cardiomyopathy using Global Proteomic Profiling and Enrichment Maps. Proteomics 2010: 1-12. Available: http://www.ncbi.nlm.nih.gov/pubmed/20127684.