Table 1 Organization of the current reference set of pathways in NFPscanner. We compiled 766 entries from 7 pathway databases — KEGG, Reactome, NCI, Biocarta, Spike, HumanCyc and PANTHER — into 49 biomedically relevant categories of basic networks, which are listed in the NFPscanner reference sets
From: NFPscanner: a webtool for knowledge-based deciphering of biomedical networks
| Source database | ||||||||
|---|---|---|---|---|---|---|---|---|
| Category | KEGG | Reactome | NCI/PID | SPIKE | HumanCyc | PANTHER | BioCarta | Total |
| Genetic Information Processing | 7 | 22 | 40 | 5 | 19 | 93 | ||
| Environmental Information Processing | 27 | 6 | 16 | 29 | 78 | |||
| Cellular Processes | 13 | 23 | 9 | 25 | 46 | 116 | ||
| Organismal Systems | 61 | 14 | 26 | 28 | 129 | |||
| Metabolism | 12 | 12 | ||||||
| Signal Transduction | 23 | 1 | 83 | 107 | ||||
| Transport Processes | 8 | 8 | ||||||
| Biosynthesis | 20 | 20 | ||||||
| Degradation | 10 | 10 | ||||||
| Modification | 15 | 15 | ||||||
| Brain | 11 | 11 | ||||||
| Cell Adhesion | 31 | 31 | ||||||
| Cytokine and Chemokine | 25 | 25 | ||||||
| Development | 7 | 7 | ||||||
| Growth Factor | 22 | 22 | ||||||
| Hormone | 16 | 16 | ||||||
| Immmune Response | 11 | 11 | ||||||
| Kinase and Phosphatase | 12 | 12 | ||||||
| Ras Superfamily | 11 | 11 | ||||||
| Second Messengers | 8 | 8 | ||||||
| Transcription Factor | 27 | 27 | ||||||
| Cell Cycle | 9 | 9 | ||||||
| DNA Damage Response | 8 | 8 | ||||||
| Hearing Related Pathways | 5 | 5 | ||||||
| Programmed Cell Death | 6 | 6 | ||||||
| Total | 108 | 108 | 199 | 28 | 46 | 72 | 205 | 766 |