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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 |
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C1: positional gene sets (browse 278 gene sets) |
Gene sets corresponding to each human chromosome and each cytogenetic band. details |
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C2: curated gene sets (browse 6290 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 sub-collections: Chemical and genetic perturbations (CGP) and Canonical pathways (CP). details |
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CGP: chemical and genetic perturbations (browse 3368 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. |
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CP: Canonical pathways (browse 2922 gene sets) |
Gene sets from pathway databases. Usually, these gene sets are canonical representations of a biological process compiled by domain experts. |
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BIOCARTA subset of CP (browse 292 gene sets) |
Canonical Pathways gene sets derived from the BioCarta pathway database. |
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KEGG subset of CP (browse 186 gene sets) |
Canonical Pathways gene sets derived from the KEGG pathway database. |
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PID subset of CP (browse 196 gene sets) |
Canonical Pathways gene sets derived from the PID pathway database. |
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REACTOME subset of CP (browse 1604 gene sets) |
Canonical Pathways gene sets derived from the Reactome pathway database. |
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WikiPathways subset of CP (browse 615 gene sets) |
Canonical Pathways gene sets derived from the WikiPathways pathway database. |
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C3: regulatory target gene sets (browse 3731 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 sub-collections: microRNA targets (MIR) and transcription factor targets (TFT). details |
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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. |
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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 |
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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 |
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TFT: transcription factor targets (browse 1133 gene sets) |
All transcription factor target prediction gene sets. Combined superset of both GTRD prediction methods and legacy sets. |
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GTRD subset of TFT (browse 523 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 |
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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 |
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C4: computational gene sets (browse 858 gene sets) |
Computational gene sets defined by mining large collections of cancer-oriented microarray data. The C4 collection is divided into two sub-collections: CGN and CM. details |
Download GMT Files Gene Symbols NCBI (Entrez) Gene IDs |
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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 |
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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. |
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C5: ontology gene sets (browse 14998 gene sets) |
Gene sets that contain genes annotated by the same ontology term. The C5 collection is divided into two sub-collections, 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 |
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GO: Gene Ontology gene sets (browse 10185 gene sets) |
All gene sets derived from Gene Ontology. details |
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BP: subset of GO (browse 7481 gene sets) |
Gene sets derived from the GO Biological Process ontology. |
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CC: subset of GO (browse 996 gene sets) |
Gene sets derived from the GO Cellular Component ontology. |
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MF: subset of GO (browse 1708 gene sets) |
Gene sets derived from the GO Molecular Function ontology. |
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HPO: Human Phenotype Ontology (browse 4813 gene sets) |
Gene sets derived from the Human Phenotype ontology. details |
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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 |
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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 |
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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 |
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VAX: vaccine reponse gene sets (browse 347 gene sets) |
Gene sets curated by the Human Immunology Project Consortium (HIPC) describing human transcriptomic immune responses to vaccinations. details |
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C8: cell type signature gene sets (browse 671 gene sets) |
Gene sets that contain curated cluster markers for cell types identified in single-cell sequencing studies of human tissue. details |
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