MSigDB v2025.1.Mm (Jun 2025)

Important Notices#

• This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2025.1 (MSigDB 2025.1.Mm).

• MSigDB v2025.1 is based on gene annotation data from Ensembl Release 114 (May 2025).

• 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 v2025.1.Mm)#

Introduction of initial M7 Immunologic Signatures Collection#

787 new gene sets have been added under the newly introduced M7 collection.

The initial release of this collection provides sets from the Cui et al. 2024 Immune Dictionary which catalogues a comprehensive overview of the cell-type specific responses to in-vivo exposure of immune cells from mouse lymph nodes to 86 different cytokines.

Gene sets were filtered to include only those sets which contained >5 and <2000 members in the raw input list in accordance with MSigDB standard practice.

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 114.

M2:CP:Reactome#

• Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of Reactome v92 (+20 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 May 10, 2025 release (+3 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 as present in the GO-basic obo file released on 2025-03-16 and NCBI gene2go annotations downloaded on 2025-05-06.

This collection is divided into three sub-collections:

• BP: GO Biological process (+143 gene sets). Gene sets derived from the Biological Process Ontology; set names are prefixed with GOBP_.
• CC: GO Cellular component (+12 gene sets). Gene sets derived from the Cellular Component Ontology; set names are prefixed with GOCC_.
• MF: GO Molecular function (+40 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.

CHIP file updates#

• MSigDB 2025.1.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 114.
• 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 8.1.0 (2025-04-18)