The 31117 gene sets in the Molecular Signatures Database (MSigDB) are
divided into 9 major collections, and several sub-collections.
See the table below for a brief description of each, and the
MSigDB Collections: Details and Acknowledgments page for more
detailed descriptions. See also the MSigDB Statistics
and the MSigDB Release Notes.
Click on the "browse gene sets" links in the table below to view the gene sets in a collection. Or download
the gene sets in a collection by clicking on the links below the "Download GMT Files" headings.
For a description of the
GMT file
format see the Data Formats in the
Documentation section.
The gene sets can be downloaded as NCBI (Entrez) Gene Identifiers or HUGO (HGNC) Gene Symbols.
An XML file containing all the MSigDB gene sets is available
on the Downloads page.
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
|
C1: positional gene sets
(browse
299 gene sets)
|
Gene sets corresponding to each human chromosome and each cytogenetic band.
details
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
C2: curated gene sets
(browse
6226 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
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
CGP: chemical and genetic perturbations
(browse
3358 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
|
CP: Canonical pathways
(browse
2868 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
|
BIOCARTA subset of CP
(browse
289 gene sets)
|
Canonical Pathways gene sets derived from the BioCarta pathway database.
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
KEGG subset of CP
(browse
186 gene sets)
|
Canonical Pathways gene sets derived from the KEGG pathway database.
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
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
|
REACTOME subset of CP
(browse
1554 gene sets)
|
Canonical Pathways gene sets derived from the Reactome pathway database.
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
WikiPathways subset of CP
(browse
587 gene sets)
|
Canonical Pathways gene sets derived from the WikiPathways pathway database.
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
C3: regulatory target gene sets
(browse
3556 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
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
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
|
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
|
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
|
TFT: transcription factor targets
(browse
958 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
|
GTRD subset of TFT
(browse
348 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
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
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
|
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
|
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
|
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
|
C5: ontology gene sets
(browse
14765 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
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
GO: Gene Ontology gene sets
(browse
10271 gene sets)
|
All gene sets derived from Gene Ontology.
details
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
BP: subset of GO
(browse
7573 gene sets)
|
Gene sets derived from the GO Biological Process ontology.
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
CC: subset of GO
(browse
1001 gene sets)
|
Gene sets derived from the GO Cellular Component ontology.
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
MF: subset of GO
(browse
1697 gene sets)
|
Gene sets derived from the GO Molecular Function ontology.
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
HPO: Human Phenotype Ontology
(browse
4494 gene sets)
|
Gene sets derived from the Human Phenotype ontology.
details
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
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
|
C7: immunologic signature gene sets
(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
|
Download GMT Files
Gene Symbols
NCBI (Entrez) Gene IDs
|
C8: cell type signature gene sets
(browse
302 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
|