Pharmacogenomics and Bioinformatics: Pharmgkb

Figures & data

Figure 1. The PharmGKB homepage has targeted searching.

The gene search box returns links to genes associated with the search term. Example queries can be viewed and include: search by gene symbol, drug, disease, drug/disease combination, Entrez Gene ID, PubMed ID and protein name [102].

Table 1. Relationships and exchange of information with other resources allows PharmGKB to focus on the subset of data relevant for pharmacogenomics.

Data type	Resources
Genes	HUGO Gene Nomenclature Committee, University of California Santa Cruz Genome Browser, NCBI, Comparative Toxicogenomics Database, GeneCards, Source, MutDB, Gen Atlas, Ensembl, UniProt
Drugs	Drugbank, WHO, OpenEye, Comparative Toxicogenomics Database, Kyoto Encyclopedia of Genes and Genomes, Chemical Entities of Biological Interest
Diseases	Medical Subject Headings, Systematized Nomenclature of Medicine
Literature	NCBI
Pathways	BioPax, Pathways Interaction Database, Reactome, Biocarta
Variants	dbSNP, Alfred, HuGENet, JSnp, HapMap, Seattle SNPs, Affymetrix
Structures	Protein Data Bank, NCBI
Other	Pharmacogenetics Research Network, US FDA, Centers for Disease Control and Prevention, GAPPNet

Table 2. Top ten PharmGKB gene, drug, disease and pathway pages for 2009.

Rank	Genes	Drugs	Diseases	Pathways
1	CYP2D6	Warfarin	Torsades de pointes	Platelet aggregation pathway (PD)
2	ABCB1	Amiodarone	Breast neoplasms	Codeine and morphine pathway (PK)
3	CYP2C9	Clopidogrel	Epilepsy	Nicotine pathway (PK)
4	CYP2C19	Oxaliplatin	Precursor cell lymphoblastic leukemia lymphoma	EGFR inhibitors pathway (PD)
5	CYP3A4	Fluoxetine	Cardiovascular diseases	Antiplatelet drug clopidogrel pathway (PK)
6	VKORC1	Capecitabine	Asthma	Bisphosphonate pathway
7	TPMT	Metoprolol	Stroke	ACE-inhibitor pathway (PD)
8	UGT1A1	Imatinib	Hypertension	Warfarin pathway (PD)
9	CYP1A2	Salbutamol	Type 2 diabetes mellitus	Warfarin pathway (PK)
10	CYP2B6	Phenylephrine	Depression	Selective serotonin reuptake inhibitors pathway

ACE: Angiotensin-converting enzyme; EGFR: EGR receptor; PD: Pharmacodynamics; PK: Pharmacokinetics.

PharmGKB www.pharmgkb.org

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