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Human MSigDB Collections
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H: 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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C1: positional gene sets (browse 302 gene sets) |
Gene sets corresponding to human chromosome cytogenetic bands. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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C2: curated gene sets (browse 7561 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 C2 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 3538 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 4023 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 292 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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KEGG_MEDICUS subset of CP (browse 658 gene sets) |
Canonical Pathways gene sets derived from the KEGG MEDICUS pathway database. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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PID subset of CP (browse 196 gene sets) |
Canonical Pathways gene sets derived from the PID pathway database. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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Reactome subset of CP (browse 1787 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 885 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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KEGG_LEGACY subset of CP (browse 186 gene sets) |
Canonical Pathways gene sets derived from the KEGG pathway database. These are considered Legacy gene sets since the introduction of the gene sets based on the more recent KEGG MEDICUS data. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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C3: regulatory target gene sets (browse 3713 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 C3 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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MIR: microRNA targets (browse 2598 gene sets) |
All miRNA target prediction gene sets. Combined superset of both miRDB prediction methods and legacy sets. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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miRDB subset of MIR (browse 2377 gene sets) |
Gene sets containing high-confidence gene-level predictions of human 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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MIR_LEGACY subset of MIR (browse 221 gene sets) |
Older gene sets that contain genes sharing putative target sites (seed matches) of human mature miRNA in their 3'-UTRs. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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TFT: transcription factor targets (browse 1115 gene sets) |
All transcription factor target prediction gene sets. Combined superset of both GTRD prediction methods and legacy sets. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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GTRD subset of TFT (browse 505 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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TFT_LEGACY subset of TFT (browse 610 gene sets) |
Older gene sets that share upstream cis-regulatory motifs which can function as potential transcription factor binding sites. Based on work by Xie et al. 2005 details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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C4: computational gene sets (browse 1006 gene sets) |
Computational gene sets defined by mining large collections of cancer-oriented expression data. The C4 collection is divided into three subcollections: 3CA, CGN and CM. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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3CA: Curated Cancer Cell Atlas (browse 148 gene sets) |
Gene sets mined from the Curated Cancer Cell Atlas (3CA) metaprograms. These sets consist of genes that are coordinately upregulated in subpopulations of cells within 24 tumor types, covering both generic and lineage specifc cellular processes. The resource underlying this collection is described in Gavish et al. 2023 |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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CGN: cancer gene neighborhoods (browse 427 gene sets) |
Gene sets defined by expression neighborhoods centered on 380 cancer-associated genes. This collection is described in Subramanian, Tamayo et al. 2005 |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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CM: cancer modules (browse 431 gene sets) |
Gene sets defined by Segal et al. 2004. Briefly, the authors compiled gene sets ('modules') from a variety of resources such as KEGG, GO, and others. By mining a large compendium of cancer-related microarray data, they identified 456 such modules as significantly changed in a variety of cancer conditions. |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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C5: ontology gene sets (browse 16228 gene sets) |
Gene sets that contain genes annotated by the same ontology term. The C5 collection is divided into two subcollections, the first derived from the Gene Ontology resource (GO) which contains BP, CC, and MF components and a second derived from the Human Phenotype Ontology (HPO). details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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GO: Gene Ontology gene sets (browse 10480 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 7583 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 1042 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 1855 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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HPO: Human Phenotype Ontology (browse 5748 gene sets) |
Gene sets derived from the Human Phenotype ontology. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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C6: oncogenic signature gene sets (browse 189 gene sets) |
Gene sets that represent signatures of cellular pathways which are often dis-regulated in cancer. The majority of signatures were generated directly from microarray data from NCBI GEO or from internal unpublished profiling experiments involving perturbation of known cancer genes. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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C7: immunologic signature gene sets (browse 5219 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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ImmuneSigDB subset of C7 (browse 4872 gene sets) |
Gene sets representing chemical and genetic perturbations of the immune system generated by manual curation of published studies in human and mouse immunology. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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VAX: vaccine response gene sets (browse 347 gene sets) |
Gene sets curated by the Human Immunology Project Consortium (HIPC) describing human transcriptomic immune responses to vaccinations. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs JSON bundle |
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C8: cell type signature gene sets (browse 866 gene sets) |
Gene sets that contain curated cluster markers for cell types identified in single-cell sequencing studies of human 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 Human gene sets in MSigDB.
NOTE: we strongly discourage running analyses against the full Human 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 Human MSigDB v2025.1.Hs contents and metadata in the form of a (ZIPped) SQLite database. See our documentation for more details on the contents and usage. | SQLite database | |
| There is also a JSON bundle containing all the Human gene sets using HUGO (HGNC) gene symbols along with some useful metadata. | JSON bundle |
