MSigDB v3.0 Release Notes

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Major changes in Release 3.0 of the Molecular Signatures Database (MSigDB) include the following:

• We have extensively reviewed and expanded the C2 collection.
• MSigDB gene sets now support human Entrez Gene IDs.
• We have modified the MSigDB XML file format to support human Entrez Gene IDs.
• A bug in the Compute Overlaps algorithm has been fixed.
• MSigDB v2.5 files archived

Gene Sets Update

The following describes the changes made to the gene set collections for MSigDB v3.0.

C1: Positional gene sets

No changes were made in the C1 gene sets.  For a description of this collection, see the <a href="http://www.broad.mit.edu/gsea/msigdb/collections.jsp">Browse Collections</a> page. 

C2: Curated gene sets (+2,075)

The C2 collection consists of gene sets collected from various sources such as online pathway databases, publications in PubMed, and knowledge of domain experts.  Gene sets in this collection have been extensively revised and expanded.
Note that all the gene set names for C2 have changed.  Many of the names used in v2.5 were confusing or wrong, so these have been clarified or corrected.  For CGP, the new naming convention is that all gene set names begin with the name of the first author of the source paper.

• CGP: chemical and genetic perturbations (3,127 gene sets). See <a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Msigdb_mapping_v2.5_to_v3">this page</a> for information about MSigDB 2.5 gene sets that have been renamed, retired, recombined, or replaced in the MSigDB 3.0 release.  These gene sets have been reviewed extensively, and during the reviewing process, we have applied changes to many existing gene sets and their contents, as follows:
  • added exact source of the gene set (e.g., Table 1)
  • added GEO or ArrayExpress ID when available
  • changed the brief description of the gene set; added links to human Entrez Gene entries and PubChem Compound entries as appropriate
    
  • used the original gene identifiers as reported in the source paper (not all gene sets did this originally)
    
  • verified the gene set contents and made corrections when necessary resolved cases of redundant gene sets
• CP: canonical pathways (840 gene sets). We have replaced all gene sets in this collection with the most up-to-date sets from BioCarta, KEGG, and Reactome.  We retrieved human pathways from the KEGG and BioCarta websites, and Reactome contributed their pathways in collaboration with MSigDB.  We applied the following filters to this data:
  • Source priority: KEGG > Reactome > BioCarta
  • Size priority: keep the set with the smaller size
  • Name length priority: keep the set with the shorter name
  • External ID priority: keep the set with the smaller ID 

C3: Motif gene sets

A user reported an error in the Brief Description of the gene set "V$NRF2_01". The error has been corrected and new Brief Description for this set appears in the new release. Members of the gene set remain unchanged.

No other changes were made in the C3 gene sets.  For a description of this collection, see the <a href="http://www.broad.mit.edu/gsea/msigdb/collections.jsp">Browse Collections</a> page.

C4: Computational gene sets

No changes were made in the C4 gene sets.  For a description of this collection, see the <a href="http://www.broad.mit.edu/gsea/msigdb/collections.jsp">Browse Collections</a> page.

C5: Gene Ontology gene sets

No changes were made in the C5 gene sets.  For a description of this collection, see the <a href="http://www.broad.mit.edu/gsea/msigdb/collections.jsp">Browse Collections</a> page.

For more information

For complete descriptions of all collections or to download the updated gene sets, go to the <a href="http://www.broad.mit.edu/gsea/msigdb/collections.jsp">Browse Collections</a> page.

Other Updates

XML Format Changes

The XML format and tags have changed.  See <a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/MSigDB_XML_description">this page</a> for more information.

Entrez IDs Now Supported

All gene sets now have Entrez IDs as well as human gene symbols, and alternate GMT files are included on the <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> page.  In addition, we have added a new CHIP file that maps Entrez IDs to human gene symbols.  Therefore, data files analyzed in GSEA can now use Entrez IDs.

Compute Overlaps Error Corrected

A user-reported bug in the Compute Overlaps algorithm has been corrected, improving the quality of the P values.

MSigDB v2.5 Files

The MSigDB v2.5 files are archived and are still available for download on the <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> page