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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 299 gene sets) |
Gene sets corresponding to each human chromosome and each cytogenetic band. details |
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C2: curated gene sets (browse 5529 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 3297 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 2232 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 289 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 1532 gene sets) |
Canonical Pathways gene sets derived from the Reactome pathway database. |
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C3: regulatory target gene sets (browse 3735 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 |
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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 1137 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 526 gene sets) |
Genes that share GTRD v19.10 (Yevshin et al. 2019) predicted transcription factor binding sites in the region -1000,+500 bp around the TSS for the indicated transcription factor. details |
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TFT_Legacy subset of TFT (browse 611 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 |
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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: GO gene sets (browse 10192 gene sets) |
Gene sets that contain genes annotated by the same GO term. The C5 collection is divided into three sub-collections based on GO ontologies: BP, CC, and MF. details |
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BP: GO biological process (browse 7530 gene sets) |
Gene sets derived from the GO Biological Process Ontology. |
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CC: GO cellular component (browse 999 gene sets) |
Gene sets derived from the GO Cellular Component Ontology. |
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MF: GO molecular function (browse 1663 gene sets) |
Gene sets derived from the GO Molecular Function Ontology. |
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C6: oncogenic signatures (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 signatures (browse 4872 gene sets) |
Gene sets that represent cell states and perturbations within the immune system. The signatures were generated by manual curation of published studies in human and mouse immunology. details |
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