DGIdb: Mining the Druggable Genome

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2013 Oct 15

PMID 24122041

Citations 278

Authors

Malachi Griffith

Obi L Griffith

Adam C Coffman

James V Weible

Josh F McMichael

Nicholas C Spies

James Koval

Indraniel Das

Matthew B Callaway

James M Eldred

Christopher A Miller

Janakiraman Subramanian

Ramaswamy Govindan

Runjun D Kumar

Ron Bose

Li Ding

Jason R Walker

David E Larson

David J Dooling

Scott M Smith

Timothy J Ley

Elaine R Mardis

Richard K Wilson

Affiliations

Soon will be listed here.

Abstract

The Drug-Gene Interaction database (DGIdb) mines existing resources that generate hypotheses about how mutated genes might be targeted therapeutically or prioritized for drug development. It provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially 'druggable' genes. DGIdb can be accessed at http://dgidb.org/.

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References

Bose R, Kavuri S, Searleman A, Shen W, Shen D, Koboldt D . Activating HER2 mutations in HER2 gene amplification negative breast cancer. Cancer Discov. 2012; 3(2):224-37. PMC: 3570596. DOI: 10.1158/2159-8290.CD-12-0349. View

Kan Z, Jaiswal B, Stinson J, Janakiraman V, Bhatt D, Stern H . Diverse somatic mutation patterns and pathway alterations in human cancers. Nature. 2010; 466(7308):869-73. DOI: 10.1038/nature09208. View

Banerji S, Cibulskis K, Rangel-Escareno C, Brown K, Carter S, Frederick A . Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012; 486(7403):405-9. PMC: 4148686. DOI: 10.1038/nature11154. View

Lim E, Pon A, Djoumbou Y, Knox C, Shrivastava S, Guo A . T3DB: a comprehensively annotated database of common toxins and their targets. Nucleic Acids Res. 2009; 38(Database issue):D781-6. PMC: 2808899. DOI: 10.1093/nar/gkp934. View

Russ A, Lampel S . The druggable genome: an update. Drug Discov Today. 2005; 10(23-24):1607-10. DOI: 10.1016/S1359-6446(05)03666-4. View

Somaiah N, Simon G . Molecular targeted agents and biologic therapies for lung cancer. J Thorac Oncol. 2011; 6(11 Suppl 4):S1758-85. DOI: 10.1097/01.JTO.0000407557.30793.a6. View

Yang W, Soares J, Greninger P, Edelman E, Lightfoot H, Forbes S . Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res. 2012; 41(Database issue):D955-61. PMC: 3531057. DOI: 10.1093/nar/gks1111. View

von Eichborn J, Murgueitio M, Dunkel M, Koerner S, Bourne P, Preissner R . PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res. 2010; 39(Database issue):D1060-6. PMC: 3013657. DOI: 10.1093/nar/gkq1037. View

Liu T, Lin Y, Wen X, Jorissen R, Gilson M . BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2006; 35(Database issue):D198-201. PMC: 1751547. DOI: 10.1093/nar/gkl999. View

10.

McDonagh E, Whirl-Carrillo M, Garten Y, Altman R, Klein T . From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med. 2011; 5(6):795-806. PMC: 3339046. DOI: 10.2217/bmm.11.94. View

11.

Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A . DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2010; 39(Database issue):D1035-41. PMC: 3013709. DOI: 10.1093/nar/gkq1126. View

12.

Gao Z, Li H, Zhang H, Liu X, Kang L, Luo X . PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics. 2008; 9:104. PMC: 2265675. DOI: 10.1186/1471-2105-9-104. View

13.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood T, Bateman A . InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2011; 40(Database issue):D306-12. PMC: 3245097. DOI: 10.1093/nar/gkr948. View

14.

Lamb J, Crawford E, Peck D, Modell J, Blat I, Wrobel M . The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006; 313(5795):1929-35. DOI: 10.1126/science.1132939. View

15.

Stephens P, Tarpey P, Davies H, Van Loo P, Greenman C, Wedge D . The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012; 486(7403):400-4. PMC: 3428862. DOI: 10.1038/nature11017. View

16.

Zhu F, Han B, Kumar P, Liu X, Ma X, Wei X . Update of TTD: Therapeutic Target Database. Nucleic Acids Res. 2009; 38(Database issue):D787-91. PMC: 2808971. DOI: 10.1093/nar/gkp1014. View

17.

Wang Y, Xiao J, Suzek T, Zhang J, Wang J, Zhou Z . PubChem's BioAssay Database. Nucleic Acids Res. 2011; 40(Database issue):D400-12. PMC: 3245056. DOI: 10.1093/nar/gkr1132. View

18.

Manning G, Whyte D, Martinez R, Hunter T, Sudarsanam S . The protein kinase complement of the human genome. Science. 2002; 298(5600):1912-34. DOI: 10.1126/science.1075762. View

19.

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin A, Kim S . The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012; 483(7391):603-7. PMC: 3320027. DOI: 10.1038/nature11003. View

20.

Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen L, Bork P . STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res. 2011; 40(Database issue):D876-80. PMC: 3245073. DOI: 10.1093/nar/gkr1011. View