Table 1.
Selected prior knowledge resources discussed in this review.
| Database | Content | Link |
|---|---|---|
| Brenda | Metabolic enzyme–substrate interactions, reaction networks and enzyme structures. | https://www.brenda-enzymes.org/ |
| CophosK | Kinase–substrate interaction inference. | http://compbio.case.edu/omics/software/cophosk/ |
| Gene Ontology | Molecular functions, biological processes and cellular components | http://geneontology.org/ |
| KEA2 | Kinase–substrate interactions from multiple resources. | http://www.maayanlab.net/KEA2/index.html |
| KEGG | Metabolic enzyme–substrate interactions and reaction networks. | https://www.genome.jp/kegg/ |
| Kinomexplorer | Kinase–substrate interaction inference. | http://kinomexplorer.info/ |
| MSigDB | Gene sets of hallmarks, positions, pathways and perturbation signatures, motifs, gene ontology, oncogenic and immunologic. | http://software.broadinstitute.org/gsea/msigdb |
| Omnipath | Protein–protein interactions pulled from various resources (mainly curated). Kinase/substrate interactions. Transcription factor–target interactions (DoRothEA). | http://omnipathdb.org/ |
| Pathway commons | Signalling and metabolic pathways from various databases. | http://www.pathwaycommons.org/ |
| PTMSigDB | Posttranslational modification signatures. | https://github.com/broadinstitute/ssGSEA2.0 |
| Reactome | Metabolic enzyme–substrate interactions and reaction networks. | https://reactome.org/ |
| STITCHdb | Chemical–proteins interactions. | http://stitch.embl.de/ |
| STRIBGdb | Protein–protein interactions pulled from various resources (curated and inferred). | https://string-db.org/ |
| Transfac | Transcription factor–target interactions. (Commercial) | http://gene-regulation.com/pub/databases.html |
| TRRUST | Transcription factor–target interaction. | https://www.grnpedia.org/trrust/ |