MSigDB 2026.2.Mm - GSEA-MSigDB Documentation

MSigDB v2026.2.Mm (Oct 2026)

Important Notices#

This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2026.2 (MSigDB 2026.2.Mm).
MSigDB v2026.2 is based on gene annotation data from Ensembl Release 116 (September 2026).
The Ensembl 116 data utilized in MSigDB v2026.2 represents the final snapshot of Ensembl's microarray probe mapping process. Future releases of MSigDB will utilize this snapshot with remapping of gene symbols.
In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.

Updates to Mouse Collections (MSigDB v2026.2.Mm)#

M1: Positional gene sets#

As previously noted in the MSigDB v2022.1.Mm Release Notes the underlying data for the M1 collection remains based on the cytogenetic band annotations provided in the Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotations for GRCm39 remain unavailable, however gene identifiers have been updated to Ensembl 116.

M2:CGP#

A signature describing H3K9ME3 mediated senesence submitted by Clemens Schmitt. This set has also been added to the C2:CGP collection for comparative analysis. See: Schleich K, Kase J, Dörr JR, Trescher S, Bhattacharya A, Yu Y, Wailes EM, Fan DNY, Lohneis P, Milanovic M, Lau A, Lenze D, Hummel M, Chapuy B, Leser U, Reimann M, Lee S, Schmitt CA. H3K9me3-mediated epigenetic regulation of senescence in mice predicts outcome of lymphoma patients. Nat Commun. 2020 Jul 20;11(1):3651. doi: 10.1038/s41467-020-17467-z. PMID: 32686676; PMCID: PMC7371731.

M2:CP:Reactome#

Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of Reactome v97 (+17 gene sets).
As previously described in the Reactome release notes for MSigDB 7.0, in order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on Jaccard coefficients and distance from the top level of the Reactome event hierarchy.

M2:CP:WikiPathways#

WikiPathways gene sets have been updated to the October 10, 2026 release (-2 gene sets).

M5: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 at the time of release production using annotations in the GO-basic obo file released on 2026-07-26 and NCBI gene2go annotations downloaded on 2026-09-30.

This collection is divided into three sub-collections:

BP: GO Biological process (-43 gene sets). Gene sets derived from the Biological Process Ontology; set names are prefixed with GOBP_.
CC: GO Cellular component (+21 gene sets). Gene sets derived from the Cellular Component Ontology; set names are prefixed with GOCC_.
MF: GO Molecular function (+46 gene sets). Gene sets derived from the Molecular Function Ontology; set names are prefixed with GOMF_.

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

The gene sets generated for the GO subcollections have been derived utilizing a new construction process. This process corrects an error identified with the exclusion of genes specifically annotated with the "NOT" annotation qualifier. Previously this small subset of genes were not properly excluded from their associated GO term.

M5:MPO (Mammalian Phenotype Ontology)#

MSigDB 2026.2 reorganizes the previous M5:MPT subcollection to accommodate additional data from the Mammalian Phenotype Ontology Resource. Previously the MPT subcollection was produced through manual selection of ontology terms containing the "tumor" descriptor. This subcollection now resides under M5:MPO:MPT and specifically reflects a redundancy filtered subset of tumor associated terms descended from the "neoplasm" (MP:0002006) ontology term. This resulted in the exclusion of 16 redundant sets.

A new subcollection M5:MPO:MP has been added which contains a redundancy filtered component of the remainder of the Mammalian Phenotype Ontology (+6757 gene sets), where the neoplasm descended terms have been excluded. This reflects the "generic" phenotype terms and their associated genes.

Both MP and MPT subcollections utilize data from the 2026-07-22 release of the Mammalian Phenotype Ontology database.

CHIP file updates#

MSigDB 2026.2.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 116.
Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to Alliance of Genome Resources orthology database release 9.1.0 (2026-09-01)