hgsc: The Hallmark collection from the MSigDB

In DavisLaboratory/enrichnets: Visualising Set Enrichment Analysis Results

The Hallmark collection from the MSigDB

Description

The molecular signatures database (MSigDB) is a collection of over 25000 gene expression signatures. Signatures in v7.2 are divided into 9 categories. The Hallmarks collection contains gene expression signatures representing molecular processes that are hallmarks in cancer development and progression.

Usage

hgsc

Format

A GeneSetCollection object with 50 GeneSet objects representing the 50 Hallmark gene expression signatures.

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.

DavisLaboratory/enrichnets documentation built on Feb. 2, 2024, 9:14 a.m.