CGM.Cat {bionetdata} | R Documentation

## 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://www.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];

[Package bionetdata version 1.0.1 Index]