is a Data Source.
Geneshot is a search engine from the Ma'ayan Laboratory that takes arbitrary search terms and returns human genes ranked by how often they are co-mentioned with those terms in PubMed, using GeneRIF and the automatically generated AutoRIF gene-publication associations. It also predicts further related genes from gene-gene similarity matrices built from ARCHS4 co-expression, Tagger literature co-occurrence, Enrichr gene-list co-occurrence, and GeneRIF/AutoRIF co-mentions. Results can be filtered by druggable genome families.
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No external IDs available
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| geneshot.portal | Geneshot Web Application | geneshot | Graphical Interface | http | Web search engine that returns genes ... |
| geneshot.api | Geneshot API | api.html | Programming Interface | json | REST API with POST endpoints to searc... |
| geneshot.downloads | Geneshot Downloads | download.html | Product | http | Download page for the GeneRIF and Aut... |
| geneshot.generif | GeneRIF Gene-Publication Associations | generif.tsv (13.9 MB) | Product | tsv | Human gene to PubMed article associat... |
| geneshot.autorif | AutoRIF Gene-Publication Associations | autorif.tsv (597.8 MB) | Product | tsv | Automatically generated human gene to... |
| geneshot.archs4-correlation | ARCHS4 Gene Co-expression Matrix | correlation.tsv.zip (4.0 GB) | Product | tsv | Gene-gene correlation matrix from ARC... |
| geneshot.enrichr-cooccurrence | Enrichr Gene Co-occurrence Matrix | list_off_co.tsv (1.5 GB) | Product | tsv | Gene-gene co-occurrence matrix comput... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| drugenrichr.libraries | DrugEnrichr Drug Set Libraries | datasetStatistics (4.2 KB) | Product | json | had primary source | Statistics for the 29 drug set librar... |
| reprotox-kg.graph.core | ReproTox-KG Core Graph | reprotox_serialization.valid.json (1.6 MB) | Graph | json | had primary source | Core ReproTox-KG graph linking birth ... |
| reprotox-kg.graph.geneshot-hpo | ReproTox-KG GeneShot HPO-Gene Graph | Geneshot_HPO_to_Gene.valid.json (6.9 MB) | Graph | json | had primary source | Birth defect phenotype to gene associ... |
| drugmonizome.libraries ⚠ | Drugmonizome Drug Set Libraries | libraries | Product | json | was derived from | The 35 Drugmonizome drug set librarie... |
Geneshot, from the Ma’ayan Laboratory at the Icahn School of Medicine at Mount Sinai, ranks human genes by their relevance to any search terms. It queries PubMed through NCBI E-utilities and cross-references the matching articles with gene-publication associations from GeneRIF (about 396,000) or AutoRIF (about 4.9 million), an automated expansion built by querying PubMed with every human gene symbol. Genes are ranked by how often they are co-mentioned with the search terms.
Geneshot predicts further related genes from gene-gene similarity matrices: ARCHS4 RNA-seq co-expression, Tagger literature co-occurrence, Enrichr gene-list co-occurrence, and GeneRIF/AutoRIF co-mentions. Results can be filtered to druggable genome families (kinases, ion channels, and GPCRs, including understudied members). The association files and similarity matrices are downloadable; the download page lists older, smaller file sizes than the files now served.
Geneshot is available as a web application and a REST API. Its help page states that the source code is available under the Apache License 2.0 and that commercial users should contact Mount Sinai Innovation Partners, but the GitHub repository it links (MaayanLab/geneshot) returned 404 when checked on 2026-10-10. Geneshot feeds the GeneShot HPO-gene graph in ReproTox-KG.
Created: October 10, 2026 | Last modified: October 10, 2026