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Mouse MSigDB Collections
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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 |
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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 |
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M2: curated gene sets (browse 2733 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 subcollections: Chemical and genetic perturbations (CGP) and Canonical pathways (CP). details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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CGP: chemical and genetic perturbations (browse 980 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 |
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CP: Canonical pathways (browse 1753 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 |
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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 |
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Reactome subset of CP (browse 1309 gene sets) |
Canonical Pathways gene sets derived from the Reactome pathway database. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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WikiPathways subset of CP (browse 192 gene sets) |
Canonical Pathways gene sets derived from the WikiPathways pathway database. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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M3: regulatory target gene sets (browse 2047 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 subcollections: microRNA targets (MIR) and transcription factor targets (TFT). details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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miRDB gene sets (browse 1768 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 |
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GTRD gene sets (browse 279 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 |
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M5: ontology gene sets (browse 10872 gene sets) |
Gene sets that contain genes annotated by the same ontology term. The M5 collection is divided into three subcollections 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 |
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GO: Gene Ontology gene sets (browse 10780 gene sets) |
All gene sets derived from Gene Ontology. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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BP: subset of GO (browse 7855 gene sets) |
Gene sets derived from the GO Biological Process ontology. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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CC: subset of GO (browse 1040 gene sets) |
Gene sets derived from the GO Cellular Component ontology. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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MF: subset of GO (browse 1885 gene sets) |
Gene sets derived from the GO Molecular Function ontology. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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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 |
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M7: immunologic signature gene sets (browse 787 gene sets) |
Gene sets that represent cell states and perturbations within the immune system. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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M8: cell type signature gene sets (browse 233 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 |
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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 |
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| The Mouse MSigDB v2025.1.Mm contents and metadata in the form of a (ZIPped) SQLite database. See our documentation for more details on the contents and usage. | (ZIPped) SQLite database | |
| There is also a JSON bundle containing all the Mouse gene sets using MGI gene symbols along with some useful metadata. | JSON bundle |
