The 5452 gene sets in the Molecular Signatures Database (MSigDB) are
divided into 5 major collections:
C1: positional gene sets
(browse 386 gene sets) |
Gene sets corresponding to each human chromosome and each cytogenetic band that has at least one gene. (Cytogenetic locations were parsed from HUGO, October 2006, and Unigene, build 197. When there were conflicts, the Unigene entry was used.) These gene sets are helpful in identifying effects related to chromosomal deletions or amplifications, dosage compensation, epigenetic silencing, and other regional effects.
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C2: curated gene sets
(browse 1892 gene sets) |
Gene sets collected from various sources such as online pathway databases, publications in PubMed, and knowledge of domain experts. The gene set page for each gene set lists its source.
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CGP: chemical and genetic perturbations
(browse 1186 gene sets) |
Gene sets that represent gene expression signatures of genetic and chemical perturbations. A number of these gene sets come in pairs: an xxx_UP (xxx_DN) gene set representing genes induced (repressed) by the perturbation. The gene set page for each gene set lists the PubMed citation on which it is based.
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CP: canonical pathways
(browse 639 gene sets) |
Gene sets from the pathway databases. Usually, these gene sets are canonical representations of a biological process compiled by domain experts.
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C3: motif gene sets
(browse 837 gene sets) |
Gene sets that contain genes that share a cis-regulatory motif that is conserved across the human, mouse, rat, and dog genomes. The motifs are catalogued in Xie, et al. (2005, Nature 434, 338–345) and represent known or likely regulatory elements in promoters and 3'-UTRs. These gene sets make it possible to link changes in a microarray experiment to a conserved, putative cis-regulatory element.
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MIR: microRNA targets
(browse 222 gene sets) |
Gene sets that contain genes that share a 3'-UTR microRNA binding motif.
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TFT: transcription factor targets
(browse 500 gene sets) |
Gene sets that contain genes that share a transcription factor binding site defined in the TRANSFAC (version 7.4, http://www.gene-regulation.com/) database. Each of these gene sets is annotated by a TRANSFAC record.
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C4: computational gene sets
(browse 883 gene sets) |
Computational gene sets defined by mining large collections of cancer-oriented microarray data.
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CM: cancer modules
(browse 456 gene sets) |
Gene sets defined by Segal et al. (Nature Genetics 36, 1090 ? 1098, 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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CGN: cancer gene neighborhoods
(browse 427 gene sets) |
Gene sets defined by expression neighborhoods centered on 380 cancer-associated genes (Brentani, Caballero et al. 2003). This collection is identical to that previously reported in (Subramanian, Tamayo et al. 2005).
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C5: GO gene sets
(browse 1454 gene sets) |
Gene sets are named by GO term and contain genes annotated by that term. GSEA users: Gene set enrichment analysis identifies gene sets consisting of co-regulated genes; GO gene sets are based on ontologies and do not generally consist of co-regulated genes.
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BP: GO biological process
(browse 825 gene sets) |
Gene sets derived from the Biological Process Ontology (http://www.geneontology.org/GO.process.guidelines.shtml).
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MF: GO molecular function
(browse 396 gene sets) |
Gene sets derived from the Molecular Function Ontology (http://www.geneontology.org/GO.function.guidelines.shtml).
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CC: GO cellular component
(browse 233 gene sets) |
Gene sets derived from the Cellular Component Ontology (http://www.geneontology.org/GO.component.guidelines.shtml).
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