Table 4.
Pathway databases.
| Pathway Databases | Full name | Comments | Cost | Visualization Capability | Website | Ref |
|---|---|---|---|---|---|---|
| KEGG pathway | Kyoto Encyclopedia of Genes and Genomes Pathway | Manually drawn pathway maps with different organisms. | Free | Y | www.genome.ad.jp/kegg/kegg2.html | [59] |
| The Cancer Cell Map | - | Ten human cancer-related signaling pathways. | Free | Cytoscape | cancer.cellmap. org/cellmap | N/A |
| Reactome | - | Biological pathways that include experimentally confirmed, manually inferred, and electronically inferred reactions. | Free | Skypainter | www.reactome.org | [62] |
| HPRD | Human Protein Reference Database | Ten human cancer signaling pathways and 10 immune system signaling pathway. | Free | GenMAPP | www.hprd.org | [54] |
| BioCarta | Charting Pathways of Life | Graphical display of known and suggested pathways. | Free | Y | www.biocarta.com/genes/index.asp | N/A |
| STKE | Signal Transduction Knowledge Environment | Database of cellular signaling pathways. | Free | SVG | stke.sciencemag.org | [101] |
| PharmGKB | The Pharmacogenetics and Pharmacogenomics Knowledge Base | Database to explore relationships among drugs, diseases and genes, including their variations and gene products. | Free | Y | www.pharmgkb.org | [102] |
| Panther Classification System | Protein Analysis Through Evolutionary Relationships | Predict protein function and contains over 139 pathways mapped to protein sequences. | Free | CellDesigner | www.pantherdb.org/pathway | [103] |
| MetaCyc | Metabolic Encyclopedia of enzymes and pathways | Non-redundant, experimentally determined pathways from more than 900 different organisms. | Free | Y | metacyc.org | [104] |
| aMAZE | - | Molecular interactions and cellular processes. | Free | N | www.scmbb.ulb.ac.be/amaze | [105] |
| CGAP | Cancer Genome Anatomy Project | Pathways are from BioCarta and KEGG. | Free | Y | cgap.nci.nih.go v/Pathways | [106] |
| INOH Pathway Database | Integrating Network Objects with Hierarchies | Pathway database of different organisms which organize pathway objects in an ontology-based system. | Free | INOH Client tool | www.inoh.org | N/A |