MSigDB v3.0 Release Notes

<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> | <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> | Documentation | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>

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

• The C2 gene set collection was extensively reviewed, revised, and expanded
  
• The XML format of the database was changed
• Gene sets now use both gene symbols and Entrez IDs
• Alternate GMT files are available for all gene sets on the <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> page
• The bug in the Compute Overlays algorithm has been corrected
• MSigDB v2.5 files are archived on the <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> page
  

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.

• CGP: chemical and genetic perturbations (3,127 gene sets). See <a href="javascript:void(0);/*1280433036809*/">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
    
  • changed the gene set name
  • 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

No 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.