MSigDB v7.5.1 (Jan 2022)

This page describes the changes made to the gene set collections for Release 7.5.x of the Molecular Signatures Database (MSigDB). This release contains updates to: C1, GO, HPO, and Reactome, as well as the addition of curated sets to C8 and user submitted sets to C2:CGP. This update incorporates the removal of clone based gene IDs introduced in Ensembl 104.

Note: Due to substantial changes introduced in MSigDB 7.0, using GSEA 4.0.0+ is recommended when utilizing MSigDB 7.0+ resources. Advisory: It is strongly recommended that users of MSigDB 7.5 always use the GSEA "Collapse/Remap to gene symbols" feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than Ensembl v105/GENCODE v39.

Specific Updates in the MSigDB 7.5.1 Patch Release (Jan 2022)#

C2:CGP and C2:CP:WikiPathways#

MSigDB 7.5 Initial Release (Jan 2022)#

Updates to Collections#


Updated human gene annotations to Ensembl 105 (+21 gene sets).


Gene sets contributed by the following individuals have been added to C2:CGP



WikiPathways gene sets have been updated to the January 10, 2022 release (+47 gene sets).


As a result of Ensembl gene annotations, 5 gene sets were removed from GTRD as they no fall below the the maximum number genes threshold (<2000 genes). (-5)

C5:GO (Gene Ontology)#

Gene sets in these sub-collections are derived from the controlled vocabulary of the Gene Ontology (GO) project: The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology (Nature Genet 2000). The gene sets are named by GO term and contain genes annotated by that term. This collection has been updated to the most recent GO annotations as present in the GO-basic obo file released on 2021-12-15 and NCBI gene2go annotations downloaded on 2022-01-03.

This collection is divided into three sub-collections:

These updates were generated in accordance with the procedure described in the GO release notes for MSigDB 7.0.

C5:HPO (Human Phenotype Ontology)#

Gene sets in this sub-collection have been updated to reflect the 2021-10-10 release of the Human Phenotype Ontology database (+258 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.

C8: cell type signature gene sets#

Added eye gene sets from Gautam and Hamashima et al. 2021. Multi-species single-cell transcriptomic analysis of ocular compartment regulons. (+29 gene sets)

Gene Set Corrections#

CHIP file updates#