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GSS Input: MSigDB Annotation

Description

This data collection encompasses five human gene set collections from the Molecular Signatures Database (MSigDB):

• C1: positional gene sets corresponding to each human chromosome and each cytogenetic band that has at least one gene
• C2: curated gene sets collected from various sources such as KEGG, GO, online pathway databases, publications in PubMed, and knowledge of domain experts
• C3: motif gene sets that contain genes that share a cis-regulatory motif that is conserved across the human, mouse, rat, and dog genomes
• C4: computational gene sets defined by mining large collections of cancer-oriented microarray data
• C5: GO term gene sets are named by GO term, containing genes annotated by that term

Instructions

1. Download msigdb_v2.5.xml or from Broad Institute's website (free registration required) msigdb_v2.5.xml.
2. Put the msigdb_v2.5.xml file in the directory GeneSetStats/ExprData

Rights

There are no restrictions on the use of this data (which was originally obtained from the MSigDB database). To cite use of MSigDB, please reference Subramanian et al (2005) and also the source for the gene set as listed on the gene set page.

Citation

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci 2005, 102:15545-15550.