is a Data Source.
The Molecular Signatures Database (MSigDB) is a comprehensive collection of tens of thousands of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. MSigDB includes curated gene sets from pathway databases, gene ontology annotations, hallmark gene sets, immunologic signatures, regulatory target sets, and cell type-specific signatures derived from single-cell sequencing studies. Available for both human and mouse, with the current public site listing Human MSigDB v2026.1.Hs and Mouse MSigDB v2026.1.Mm.
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infores:msigdb
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| msigdb.browser | MSigDB Web Browser | msigdb | GraphicalInterface | http | Web interface for browsing, searching... |
| msigdb.downloads.human ⚠ | MSigDB Human Gene Sets Downloads | downloads.jsp#msigdb | Product | mixed | Downloadable gene set files in GMT, X... |
| msigdb.downloads.mouse ⚠ | MSigDB Mouse Gene Sets Downloads | downloads.jsp#msigdb | Product | mixed | Downloadable gene set files for mouse... |
| msigdb.collections.human | MSigDB Human Collections Documentation | collections.jsp | DocumentationProduct | http | Human MSigDB collection descriptions ... |
| msigdb.collections.mouse | MSigDB Mouse Collections Documentation | collections.jsp | DocumentationProduct | http | Mouse MSigDB collection descriptions ... |
| msigdb.investigate | MSigDB Investigate Tool | annotate.jsp | GraphicalInterface | http | Interactive tool for computing overla... |
| msigdb.gene_families | MSigDB Gene Families Tool | gene_families.jsp | GraphicalInterface | http | Tool for categorizing gene set member... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| ubkg.neo4j | UBKG Neo4j Docker Distribution | ubkg-downloads.xconsortia.org | GraphProduct | ❔ | had primary source | Turnkey neo4j distributions that depl... |
| ubkg.csv | UBKG Ontology CSV Files | ubkg-downloads.xconsortia.org | GraphProduct | csv | had primary source | Ontology CSV files that can be import... |
| obo-db-ingest.msigdb.tsv | msigdb Nodes TSV | msigdb.tsv (3.0 MB) | Product | tsv | had primary source | msigdb Nodes TSV |
| prokn.msigdb.msigdb.chr_band_contains_gene.gene.edges | ProKN MSIGDB Chromosome Band Edges | DDKG_MSIGDB.MSigDB.CHR_BAND_CONTAINS_GENE.Gene.edges.csv (4.9 MB) | GraphProduct | csv | had primary source | MSIGDB chromosome band contains gene ... |
| prokn.msigdb.msigdb.has_marker_gene.gene.edges | ProKN MSIGDB Marker Gene Edges | DDKG_MSIGDB.MSigDB.HAS_MARKER_GENE.Gene.edges.csv (23.7 MB) | GraphProduct | csv | had primary source | MSIGDB marker gene edges |
| prokn.msigdb.msigdb.has_signature_gene.gene.edges | ProKN MSIGDB Signature Gene Edges | DDKG_MSIGDB.MSigDB.HAS_SIGNATURE_GENE.Gene.edges.csv (1.6 MB) | GraphProduct | csv | had primary source | MSIGDB signature gene edges |
| prokn.msigdb.msigdb.pathway_associated_with_gene.gene.edges | ProKN MSIGDB Pathway Gene Edges | DDKG_MSIGDB.MSigDB.PATHWAY_ASSOCIATED_WITH_GENE.Gene.edges.csv (120.1 MB) | GraphProduct | csv | had primary source | MSIGDB pathway associated with gene e... |
| prokn.msigdb.msigdb.targets_expression_of_gene.gene.edges | ProKN MSIGDB Targets Expression Edges | DDKG_MSIGDB.MSigDB.TARGETS_EXPRESSION_OF_GENE.Gene.edges.csv (149.2 MB) | GraphProduct | csv | had primary source | MSIGDB targets expression of gene edges |
| cfde-gse.graph | CFDE-GSE Knowledge Graph | ❔ | GraphProduct | neo4j | had primary source | Neo4j knowledge graph containing inte... |
| cfde-gse.genesets | CFDE Gene Set Collections | downloads | Product | ❔ | had primary source | Standardized gene set collections fro... |
| pathwaycommons.biopax | Integrated BioPAX Model | pc-biopax.owl.gz (1.6 GB) | Product | biopax | was derived from | PC v14 integrated BioPAX Level 3 unif... |
| harmonizome.downloads | Harmonizome Downloads | download | Product | mixed | was derived from | Harmonizome 3.0 processed dataset dow... |
| harmonizome.kg-neo4j | Harmonizome Knowledge Graph Neo4j Database | harmonizome-kg.maayanlab.cloud | GraphProduct | neo4j | was derived from | Neo4j knowledge graph serialization o... |
| pathwaycommons.downloads | Pathway Commons Data Downloads | v14 | Product | mixed | was derived from | Download directory for Pathway Common... |
| pathwaycommons.sif | SIF Network Format | pc-hgnc.sif.gz (9.4 MB) | Product | sif | was derived from | PC v14 Simple Interaction Format netw... |
| pathwaycommons.gmt | GMT Gene Set Format | pc-hgnc.gmt.gz (256.4 KB) | Product | ❔ | was derived from | PC v14 Gene Matrix Transposed gene se... |
| pathwaycommons.txt | Extended SIF TXT Format | pc-hgnc.txt.gz (110.3 MB) | Product | txt | was derived from | PC v14 tab-delimited extended SIF nod... |
| biobtree.api | BioBTree REST API | api | ProgrammingInterface | http | had primary source | REST API for searching identifiers an... |
The Molecular Signatures Database (MSigDB) is a comprehensive resource of tens of thousands of annotated gene sets designed for use with Gene Set Enrichment Analysis (GSEA) software. Developed as a joint project between UC San Diego and the Broad Institute, MSigDB provides systematic gene set collections that enable researchers to interpret genome-wide expression profiles and identify coordinate changes in gene expression.
MSigDB gene sets are designed for direct use with GSEA (Gene Set Enrichment Analysis) software to identify whether predefined sets of genes show statistically significant, concordant differences between two biological states.
Currently funded by NCI’s Informatics Technology for Cancer Research (ITCR) program.
MSigDB welcomes suggestions and contributions of new gene sets from the research community.
Created: October 30, 2025 | Last modified: June 02, 2026