MSigDB v2025.1.Hs (Jun 2025)

Important Notices#

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

• 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 Human Collections (MSigDB v2025.1.Hs)#

C1: positional gene sets#

Updated human gene annotations to Ensembl 114.

C2:CGP#

44 Gene sets have been added to C2:CGP, these gene sets consist of:

• A set describing YAP/TAZ-TEAD Signaling from Kanai et al. 2024
• Sets describing various cell cycle states from Pulver and Forey et al. (preprint)
• Sets describing EGFR-TKI treatment in EGFR-mutant non-small cell lung cancer from Figarol et al. 2024
• A set describing a bone-specific cellular expression signature from Thaler et al. 2022
• Sets describing platelet hyperactivity from Berger et al. 2024
• Sets describing renal cell carcinoma from Zhang et al. 2025
• A set describing a mitochondrial signature associated with endometrial cancer prognosis from Lin et al. 2025
• Sets describing adipose tissue mass and composition from Konigorski et al. 2022
• Sets describing a free radical associated gene signature associated with sepsis risk from Feng et al. 2024
• A set describing the process of ferroptosis mediated by LNCRNAs in Lung Adenocarcinoma from Dong et al. 2024
• A set describing genes upregulated in cancer cell lines sensitive to N-myristoyltransferase (NMT) inhibition from Beauchamp et al. 2024
• Sets describing severe COVID19 risk from Armignacco et al. 2024

C2:CP:Reactome#

• Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of Reactome 92 (+51 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 subcollection we applied a filtering procedure based on Jaccard coefficients and distance from the top level of the Reactome event hierarchy.

C2:CP:WikiPathways#

WikiPathways gene sets have been updated to the May 10, 2025 release (+55 gene sets).

C3:TFT:GTRD#

• Renamed CRELD1_TARGET_GENES to REL_ALT_TARGET_GENES to correct an upstream annotation error in GTRD source data. REL_TARGET_GENES and REL_ALT_TARGET_GENES represent CHIP-Seq targets of the same antibody in differing tissue contexts with REL_ALT_TARGET_GENES inadvertently misattributed.

C5:GO (Gene Ontology)#

Gene sets in these subcollections 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 subcollections:

• BP: GO Biological process (-25 gene sets). Gene sets derived from the Biological Process Ontology; set names are prefixed with GOBP_.
• CC: GO Cellular component (+16 gene sets). Gene sets derived from the Cellular Component Ontology; set names are prefixed with GOCC_.
• MF: GO Molecular function (+35 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.

C5:HPO (Human Phenotype Ontology)#

Gene sets in this subcollection have been updated to reflect the 2025-05-06 release of the Human Phenotype Ontology database (+95 gene sets). This subcollection has been redundancy filtered through a procedure comparable to that of the GO and Reactome subcollections.

Note that this release contains a continuity breaking change for the set HP_ABNORMAL_AFFECT (EXACT_SOURCE HP:5200261), this set has been renamed to HP_ABNORMAL_DEMEANOR in accordance with an upstream change from the parent resource, and replaced with a new HP_ABNORMAL_AFFECT set with EXACT_SOURCE HP:0025766.

C8 (Cell Type Signatures)#

Set additions: - Gene sets describing cell identities in conventional central chondrosarcoma and normal skeletal tissue from Su et al. 2024 (+26 gene sets)

Corrections: - Fixed an error in the annotation of DESCARTES_FETAL_ gene sets that previously incorrectly reported their origin species as Mus musculus instead of Homo sapiens

CHIP file updates#

• MSigDB 2025.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 114.
• Gene orthology annotations for mapping mouse 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)