Mouse MSigDB Collections

The 15918 gene sets in the Mouse Molecular Signatures Database (MSigDB) are divided into 6 major collections, and several sub-collections. See the table below for a brief description of each, and the Mouse MSigDB Collections: Details and Acknowledgments page for more detailed descriptions. See also the MSigDB Release Notes.

Click on the "browse gene sets" links in the table below to view the gene sets in a collection. Or download the gene sets in a collection by clicking on the links below the "Download Files" headings. For a description of the GMT file format see the Data Formats in the Documentation section. The gene sets can be downloaded as NCBI (Entrez) Gene Identifiers or MGI Gene Symbols. There are also JSON bundles containing the MGI Gene Symbols along with some useful metadata. An XML file containing all the Mouse MSigDB gene sets is available as well.

MH: hallmark gene sets
(browse 50 gene sets)
Hallmark gene sets summarize and represent specific well-defined biological states or processes and display coherent expression. These gene sets were generated by a computational methodology based on identifying overlaps between gene sets in other MSigDB collections and retaining genes that display coordinate expression. details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
M1: positional gene sets
(browse 341 gene sets)
Gene sets corresponding to mouse chromosome cytogenetic bands. details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
M2: curated gene sets
(browse 2619 gene sets)
Gene sets in this collection are curated from various sources, including online pathway databases and the biomedical literature. Many sets are also contributed by individual domain experts. The gene set page for each gene set lists its source. The M2 collection is divided into the following two sub-collections: Chemical and genetic perturbations (CGP) and Canonical pathways (CP). details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
CGP: chemical and genetic perturbations
(browse 932 gene sets)
Gene sets represent expression signatures of genetic and chemical perturbations. A number of these gene sets come in pairs: xxx_UP (and xxx_DN) gene set representing genes induced (and repressed) by the perturbation. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
CP: Canonical pathways
(browse 1687 gene sets)
Gene sets from pathway databases. Usually, these gene sets are canonical representations of a biological process compiled by domain experts. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
BioCarta subset of CP
(browse 252 gene sets)
Canonical Pathways gene sets derived from the BioCarta pathway database. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
Reactome subset of CP
(browse 1249 gene sets)
Canonical Pathways gene sets derived from the Reactome pathway database. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
WikiPathways subset of CP
(browse 186 gene sets)
Canonical Pathways gene sets derived from the WikiPathways pathway database. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
M3: regulatory target gene sets
(browse 2042 gene sets)
Gene sets representing potential targets of regulation by transcription factors or microRNAs. The sets consist of genes grouped by elements they share in their non-protein coding regions. The elements represent known or likely cis-regulatory elements in promoters and 3'-UTRs. The M3 collection is divided into two sub-collections: microRNA targets (MIR) and transcription factor targets (TFT). details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
miRDB gene sets
(browse 1769 gene sets)
Gene sets containing high-confidence gene-level predictions of mouse miRNA targets as catalogued by miRDB v6.0 algorithm (Chen and Wang, 2020). details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
GTRD gene sets
(browse 273 gene sets)
Genes that share GTRD (Kolmykov et al. 2021) predicted transcription factor binding sites in the region -1000,+100 bp around the TSS for the indicated transcription factor. details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
M5: ontology gene sets
(browse 10652 gene sets)
Gene sets that contain genes annotated by the same ontology term. The M5 collection is divided into three sub-collections derived from the Gene Ontology resource (GO) which contains BP, CC, and MF components. details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
GO: Gene Ontology gene sets
(browse 10560 gene sets)
All gene sets derived from Gene Ontology. details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
BP: subset of GO
(browse 7775 gene sets)
Gene sets derived from the GO Biological Process ontology. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
CC: subset of GO
(browse 1039 gene sets)
Gene sets derived from the GO Cellular Component ontology. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
MF: subset of GO
(browse 1746 gene sets)
Gene sets derived from the GO Molecular Function ontology. Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
MPT: tumor phenotype ontology
(browse 92 gene sets)
A subset of ontology terms from the Mammalian Phenotype Ontology database related to cancer specific phenotype terms. details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle
M8: cell type signature gene sets
(browse 214 gene sets)
Gene sets that contain curated cluster markers for cell types identified in single-cell sequencing studies of mouse tissue. details Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle



All gene sets
(browse all gene sets)
Bundles containing all mouse gene sets in MSigDB.

NOTE: we strongly discourage running analyses against the full Mouse MSigDB GMTs. We recommend using the above GMTs instead for more focused results.
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs

JSON bundle

XML bundle with full metadata