MSigDB v2024.1.Hs (Aug 2024)

Important Notices#

• This page describes updates made to the Molecular Signatures Database Human Collections for release 2024.1 (MSigDB 2024.1.Hs).

• MSigDB v2024.1 is based on gene annotation data from Ensembl Release 112 (May 2024).

• 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 v2024.1.Hs)#

C1: positional gene sets#

Updated human gene annotations to Ensembl 112 (+1 gene set).

C2:CGP#

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

• Sets describing tissue resident T cell signatures associated with better melanoma prognosis from Jiang et al. 2024
• Sets describing the immune state in Progressive Idiopathic Pulmonary Fibrosis from Unterman et al. 2024
• Sets describing the retrodifferentiation and metabolic reprogramming of human tumor hepatocytes from Fekir et al. 2019
• HUANG_AML_LSC47, a set describing genes up-regulated in AML leukemia stem cells (LSC) and predictive for outcome in AML from Huang et al. 2022
• BRAUNE_GEIST_20_GENE_NOTCH_SIG_BREAST_CANCER, a Notch transcriptomic signature designed to measure the level of Notch signaling in breast cancer from Braune et al. 2024

Corrections: - Fixed an inversion between DODD_NASOPHARYNGEAL_CARCINOMA_UP and DODD_NASOPHARYNGEAL_CARCINOMA_DN. These sets have been renamed to reflect their correct directionality.

C2:CP:KEGG_MEDICUS#

• KEGG_Medicus sets were updated to the 2023-09-23 release of the Medicus network database file (latest as of August 2024) (+39 gene sets).

C2:CP:Reactome#

• Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of Reactome v89 (+44 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 July 10, 2024 release (+39 gene sets).

C3:TFT:GTRD#

• Renamed HSD17B8_TARGET_GENES to RING2_TARGET_GENES to correct an upstream annotation error in GTRD source data
• Renamed IGLV5_37_TARGET_GENES to SS18_SSX_TARGET_GENES to correct an upstream annotation error in GTRD source data

C3:TFT:TFT_LEGACY#

• Corrected erroneous associated with the AR gene in the brief description of the set ER_Q6_01.

C4:3CA#

• One set from the prior release was excluded as a result of failure to pass mapping thresholds (-1 gene set)

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 2024-04-24 and NCBI gene2go annotations downloaded on 2024-05-15.

This collection is divided into three subcollections:

• BP: GO Biological process (-39 gene sets). Gene sets derived from the Biological Process Ontology; set names are prefixed with GOBP_.
• CC: GO Cellular component (+11 gene sets). Gene sets derived from the Cellular Component Ontology; set names are prefixed with GOCC_.
• MF: GO Molecular function (+21 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 2024-04-26 release of the Human Phenotype Ontology database (+106 gene sets). This subcollection has been redundancy filtered through a procedure comparable to that of the GO and Reactome subcollections.

C8 (Cell Type Signatures)#

Set additions: - Gene sets describing the cellular composition of human ovary from Jones et al. 2024 (+10 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 2024.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 112.
• Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to Alliance of Genome Resources orthology database release 7.1 (2024-05-01)