MSigDB v2023.2.Mm (Oct 2023)

Important Notices#

• This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2023.2 (MSigDB 2023.2.Mm).
• MSigDB v2023.2 is based on gene annotation data from Ensembl Release 110 (July 2023).
• 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 v2023.2.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.

M2:CGP#

28 Gene sets have been added to M2:CGP, these gene sets consist of:

• NABA_ gene sets which mirror the Matrisome gene sets previously included in the human database describing the extracellular matrix of normal tissues.
• New NABA_MATRISOME_ gene sets describing the extracellular matrix compostion of various tumor microenviornments.
• 13 gene sets from Zeng and Gu et al. 2022 which were found to be predictive of tumor response to immune checkpoint blockade therapy. The names of these sets are prefixed ZENG_GU_ICB_.

M2:CP:Reactome#

• Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of Reactome v86 (+10 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, 2023 release (+0 gene sets).

M3:GTRD#

One additional gene set was removed as a result of gene mapping changes (-1).

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 2023-07-27 and NCBI gene2go annotations downloaded on 2023-09-01.

This collection is divided into three sub-collections:

• BP: GO Biological process (-46 gene sets). Gene sets derived from the Biological Process Ontology; set names are prefixed with GOBP_.
• CC: GO Cellular component (+3 gene sets). Gene sets derived from the Cellular Component Ontology; set names are prefixed with GOCC_.
• MF: GO Molecular function (+32 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.

M8 cell type signature gene sets#

One additional gene set was included as a result of gene mapping changes (+1).

CHIP file updates#

• MSigDB 2023.2.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 110.
• 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 5.4 (2023-04-24)