msigdb: MSigDB canonical pathways and corresponding gene lists

In padma: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Description

Data.frame of 1322 pathways and corresponding gene symbols included in the MSigDB canonical pathways curated gene set catalog, which includes genes whose products are involved in metabolic and signaling pathways reported in curated public databases. This specifically corresponds to the 'C2 curated gene sets' catalog from MSigDB v5.2 available at http://bioinf.wehi.edu.au/software/MSigDB/ as described in the limma Bioconductor package.

Usage

data(msigdb)

Format

An object of class data.frame with two columns: geneset, which provides the 1322 MSigDB curated pathway names (e.g., 'c2_cp_BIOCARTA_41BB_PATHWAY') and symbol, which provides the comma-separated corresponding list of gene symbols.

Source

MSigDB Gene sets http://bioinf.wehi.edu.au/software/MSigDB/

References

Liberzon et al. (2011) Bioinformatics 27:12, 1739-1740. https://doi.org/10.1093/bioinformatics/btr260.

Examples

data(msigdb)
head(msigdb)

padma documentation built on Nov. 8, 2020, 4:56 p.m.