CGM.Cat: Cancer Gene Modules

In bionetdata: Biological and Chemical Data Networks

Cancer Gene Modules

Description

Cancer Gene Modules classes for the genes included in FIN.data. Annotations are taken from the GSEA MSigDB (Molecular Signatures Database) public repository:

http://www.broadinstitute.org/gsea/msigdb

The annotations are available in MSigDB C4 (computational gene sets collections) CM (cancer modules), file: c4.cgn.v3.0.symbols.gmt . This collection of gene sets is taken from a work published by Segal and colleagues aimed at the definition of a Cancer Modules Maps. According to the definition of the authors Cancer Gene Modules are groups of genes that act in concert to carry out a biological function/process. Cancer Gene Modules have been used to describe expression profiles in different tumors types in terms of the behavior of modules. Further information about specific modules can be found at: http://robotics.stanford.edu/~erans/cancer/browse_by_modules.html It is worth noting that the Cancer Gene Modules annotations contained in bionetdata covers only the 2033 genes included in FIN.data.

Usage

data(CGM.Cat)

Format

A 2033 x 10 named matrix where rows refer to human gene symbols, columns to 10 Cancer Modules classes.

Source

Original annotations (c4.cm.v3.0.symbols.gmt) are available at:

http://software.broadinstitute.org/gsea/msigdb

References

Segal E., Friedman N., Koller D. and Regev A., A module map showing conditional activity of expression modules in cancer, Nature Genetics, 36(10), 2004

Examples

data(CGM.Cat);
CGM.Cat[1:10,1:10];

bionetdata documentation built on Sept. 12, 2022, 9:05 a.m.