MSigDB v5.0 Release Notes

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New collection H: Hallmark signatures

H: Hallmarks is a new collection of 50 sets. These gene sets represent specific well defined biological states or processes and display coherent expression. The hallmark gene sets were generated by a computational methodology based on identifying gene set overlaps and extracting coherent representatives of them. Details of the procedure will become available after the manuscript describing it is accepted for publication. The hallmark gene sets reduce noise and redundancy and provide a better biological space for GSEA and other gene set-based analyses of genomic data.

We envision this collection as the starting point for exploring MSigDB resource and GSEA. This collection is an initial release of 50 hallmarks which condense information from over 4,000 original overlapping gene sets from v4.0 MSigDB collections C1 through C6. We refer to the original gene sets as “founder” sets.

Hallmark gene set pages provide links to the corresponding founder sets for more in-depth exploration. In addition, hallmark gene set pages include links to microarray data that served for refining and validation of the hallmark signatures.

Updates to C2 collection

We have removed all 132 gene sets which originated from the Munich Information Center for Protein Sequences (CORUM MIPS) database because they no longer allow redistribution of this information. Previously, these sets were part of Canonical Pathways (CP) in the C2 collection.

Four (4) new gene sets curated from papers were added to the C2:CGP (Chemical and Genetic Perturbations) sub-collection.

Updates to C4: Cancer Modules

We have fixed an error in the external link URLs for all 431 sets in the C4:CM (Cancer Modules) sub-collection.

Viewing previous versions of MSigDB

Files from previous versions of MSigDB (v3.1, v3.0, v2.5, v2.1 and v1.0) are archived and available at Downloads page. You can view them through the MSigDB Browser tool in the GSEA desktop application.