Table 2.
Various databases related to diseases, genes, proteins, and drugs and other information about their data type, statistics, availability, and programmatic access.
| Database name | Type | Statistic | Availability | Programmatic access | |
|---|---|---|---|---|---|
| 1 | OMIM-21 | Gene–disease association | Autosomal – 24,944, X linked – 1331, Y linked – 63, mitochondrial – 71 | Upon request | – |
| 2 | miR2disease – 22 | miRNA–disease association | Number of miRNAs: 349 Number of diseases: 163 Number of entries: 3273 |
Open source | – |
| 3 | STITCH-23 | Chemical–Protein interaction | 0.5 million Chemicals, 9.6 million proteins, and 1.6 billion interactions | Open source | Rest API |
| 4 | HPRD-24 | Protein–protein interaction (PPI) | PPIs – 41,327, Protein expressions – 112,158, PubMed Links 453,521 | Open source | – |
| 5 | BioGRID-25 | PPI/genetic interaction | 86,000 + genes, 745 different cell lines, 127 different cell types, and 23 different phenotypes across 4 different organisms | Open source | Rest API, Blast, and more |
| 6 | DIP-26 | PPI | – | Upon request | – |
| 7 | TRED-27 | TF–gene interaction | It contains 11,660 target genes and around 14,908 target promoters | – | Sequence tool analysis |
| 8 | TRANSFAC-28 | TF–gene interaction | – | Paid | MATCH Suite |
| 9 | miRbase-29 | MicroRNA–gene interaction | 38,589 miRNA entries | Open source | Blast |
| 10 | TargetScan-30 | MicroRNA–gene interaction | – | Open source | – |
| 11 | Signaling Network-31 | Human signaling network | – | Open source | Multiple tools |
| 12 | GO-32 | Functional annotation | More than 700,000 experimentally supported | Open Source | Multiple tools |
| 13 | CMAP-33 | Microarray | library containing over 1.5 M gene expression profiles from ~5000 small-molecule compounds, and ~3000 genetic reagents, tested in multiple cell types | Open source | Rest API, multiple tools |
| 14 | Arrayexpress-34 | Microarray | It is consisted of 75,570 experiments and 25,96,304 assays | Open Source | Rest API, Blast, Multiple tools |
| 15 | GEO-35 | Microarray | Contains around 4348 datasets, 23,172 platforms, and 5,029,933 samples. | Open source | – |
| 16 | DCDB-39 | Drug combination–disease association | It contains the drug combinations of 330 approved and 1033 investigational drugs. | Open source | – |
| 17 | KEGG-40 | Pathway,disease, drug | Information can extract and stats are different for different KEGG databases | Open source | Fasta, Blast |
| 18 | ClinicalTrial.gov | Drug–disease association | It contains around 414,049 studies conducted in 220 countries | Open source | – |
| 19 | Drugs@FDA | Drug–disease association | – | Open source | – |