Reference data sources
Genomarker enrichment analysis uses curated pathway databases and gene-symbol references listed below. All data is used under its original license. We redistribute reference bundles via versioned GitHub releases; the raw source data remains the property of its original authors.
Pathway & gene-set sources
| Source | Purpose | License | Citation |
|---|---|---|---|
| Reactome Pathways | Peer-reviewed pathway database | Creative Commons Public Domain (CC0) | Milacic et al., The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research. |
| GO Biological Process | Gene Ontology biological processes | CC BY 4.0 | Ashburner et al., 2000; The Gene Ontology Consortium, 2023. |
| GO Molecular Function | Gene Ontology molecular functions | CC BY 4.0 | Ashburner et al., 2000; The Gene Ontology Consortium, 2023. |
| GO Cellular Component | Gene Ontology cellular components | CC BY 4.0 | Ashburner et al., 2000; The Gene Ontology Consortium, 2023. |
| MSigDB Hallmark | Curated 50 cancer hallmark gene sets | MSigDB license (research use; registration required for download) | Liberzon et al., 2015; Subramanian et al., 2005. |
| HGNC | Gene symbol canonicalization | No restrictions (public) | Seal et al., 2023. HGNC: a working name for the human gene nomenclature. |
MSigDB Terms of Use
Molecular Signatures Database (MSigDB) data is provided by the Broad Institute under the MSigDB Terms of Use. By using enrichment features that surface MSigDB-derived results you agree to comply with those terms, including restricting use to non-commercial academic research unless you hold a separate MSigDB commercial license, providing appropriate citation (Liberzon et al., 2015) in published work, and not redistributing MSigDB gene sets as a standalone derivative. Commercial users should obtain licensing directly from the Broad Institute.
Bundle versions
Reference data is shipped as versioned bundles. The version used for a specific enrichment run is recorded in the job's result_summary.source_version field and surfaced in the result view header.
Citing
When publishing results that rely on these sources, please cite each database according to its own citation guidelines. The links in the table above lead to upstream citation pages.