Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network

BMC Bioinformatics

Table 1 Drug2Gene data source statistics

Source database	Genes/proteins	Drugs/compounds	Relations/interactions	Unique relations in DB
CGDCP [17]	6071	3115	169154	154532 (3.534%)
ChEMBL [1]	5115	746582	2830526	2519174 (57.617%)
CTD [18]	27314	11569	89094	70944 (1.623%)
DrugBank [5]	3726	7825	17321	7338 (0.168%)
IUPHAR [19]	114	1455	651	348 (0.008%)
MICAD [20]	249	68	70	55 (0.001%)
PDSP_Ki [21]	605	5256	22790	11505 (0.263%)
PharmGKB [22]	22677	3630	78317	73064 (1.671%)
TTD [23]	1518	2418	2599	1077 (0.025%)
Uniprot [24]	86605	3693	351189	342495 (7.833%)
Ligand Expo [25]	-	7516	32511	26249 (0.600%)
HGNC [26]	24726	-	-	-
PDBsum [27]	23745	-	-	-
ChEBI [28]	-	5015	-	-
NCBI PubChem Compound [29]	-	746546	-	-
NCBI PubChem Substance [29]	-	767740	-	-
PubChem Bioassay [30]	-	-	1124637	831359 (19.014%)
Unified relations shared among two or more DBs	-	-	-	334150 (7.642%)
Total counts from all source databases	202465	2312423	4945372	4372290 (100.00%)
NCBI Gene/Entrez Gene [15]	Used for Unification/Data Integration
Homology inferred relations from NCBI HomoloGene [15]	-	-	226513	-
Total relations in Drug2Gene including homology-inferred relations	-	-	5171885	4598803

Drug2Gene is built of three entities: genes, compounds, and relations between them. The entities are extracted from 19 public source databases. Numbers of entities are listed by source database and by type of the extracted entity - genes, compounds, or relations. Most of the compound-target oriented (relational) databases provide all three types of entries in their flat files. There are also only gene-centered (HGNC, PDBsum, and NCBI Gene) and compound-centered (ChEBI, NCBI PubChem Compound, and NCBI PubChem Substance) source databases that provide only gene or compound entries. Their entities are linked by relational sources like Ligand Expo (links to proteins in PDBsum) and PubChem Bioassay (relations between genes in NCBI Gene and compounds/substances in NCBI PubChem Compound/Substance). Only entries participating in a relation are counted in this table. For data regardless participation in relations, see Additional file 1: Table S2. Dataset - November 2013. The last column shows the number of relations after data integration (and as percent of the total number of integrated relations) unique to each source database.

ISSN: 1471-2105