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)


Following collections were used:
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.
file: c2.cp.v2.5.symbols.gmt
639 canonical pathways
(subset of MSigDB.c2.all)
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
file: c3.tft.v2.5.symbols.gmt
500 transcription factor targets
(subset of MSigDB.c3.all)
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:
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: