msigdb: The Molecular Signatures Database (MSigDB)

In DavisLaboratory/msigdbR: An ExperimentHub Package for the Molecular Signatures Database (MSigDB)

The Molecular Signatures Database (MSigDB)

Description

This ExperimentHub package contains gene expression signatures from the molecular signatures database (MSigDB) for versions >= 7.2. Collections for human and mouse are currently supported in this package. The mouse version was developed in conjunction with Gordon K Smyth and Alexandra Garnham, and reflects the collections available from WEHI (https://bioinf.wehi.edu.au/MSigDB/).

Format

A GeneSetCollection object composed of GeneSet objects representing all non-empty gene expression signatures from the molecular signatures database (MSigDB).

Details

The molecular signatures database (MSigDB) is a collection of over 25000 gene expression signatures that are grouped into collections and sub-collections. Metadata associated with signatures is collected and stored in the data in this package.

All data in this package are stored in a GeneSetCollection object from the GSEABase package. Each gene expression signature in the collection is stored in a GeneSet object from the GSEABase package. This data does not include KEGG gene sets due to copyrights. Users can download this data using functions provided in the package (see Details).

Data in this package does not include gene sets from the KEGG database due to licensing limitations. Users can use the appendKEGG() function in this package to download KEGG gene sets directly from the MSigDB and append to existing data objects.

The mouse MSigDB is created by translating human genes to mouse homologs using annotations from the Mouse Genome Informatics (MGI) database for most gene sets. Gene sets in the collections c1 (positional gene sets) and c5 (ontologies) are recreated as information in these gene sets is organism specific. Positional gene sets are created using gene information from NCBI. Gene sets representing gene ontologies are derived from the mouse R/Bioconductor organism database (org.Mm.eg.db).

Acknowledgement

MSigDB is protected by copyright © 2004-2020 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. Use of MSigDB is subject to the terms and conditions of the Creative Commons Attribution 4.0 International License - https://creativecommons.org/licenses/by/4.0/.

MSigDB gene sets derived from BioCarta pathways are the subject of copyright © 2000-2017 BioCarta, and are subject to Biocarta's Disclaimer of Liability and of Warranties - https://data.broadinstitute.org/gsea-msigdb/msigdb/biocarta/biocarta_disclaimer_of_liability_and_of_warranties.txt

References

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., ... & Mesirov, J. P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550.

Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.

Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015). The molecular signatures database hallmark gene set collection. Cell systems, 1(6), 417-425.

Examples

library(ExperimentHub)
eh <- ExperimentHub()
msigdb_datasets <- query(eh, "msigdb")

#load data using different approaches
msigdb <- getMsigdb('hs', 'SYM')
msigdb <- eh[["EH5421"]]

DavisLaboratory/msigdbR documentation built on July 27, 2023, 4 p.m.