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DGIdb: mining the druggable genome

Nature Methods volume 10, pages 1209–1210 (2013)Cite this article

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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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Figure 1: Druggability of genes recurrently mutated in breast cancer.

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Acknowledgements

We thank the creators of each source we used as input and all users of DGIdb who have contributed feedback, R. Altman, Stanford University and PharmGKB for granting us a license to mine their data, W. Pao of My Cancer Genome for agreeing to collaborate with us, and the individuals who participated in research that led to the breast cancer data used to demonstrate the utility of DGIdb. This work was funded by an US National Institutes of Health NHGRI center grant (U54 HG003079) to R.K.W.

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Author notes

  1. Malachi Griffith and Obi L Griffith: These authors contributed equally to this work.

Authors and Affiliations

  1. The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA

    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, Li Ding, Jason R Walker, David E Larson, David J Dooling, Scott M Smith, Timothy J Ley, Elaine R Mardis & Richard K Wilson

  2. Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA

    Malachi Griffith, Li Ding, David E Larson, Elaine R Mardis & Richard K Wilson

  3. Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, USA

    Obi L Griffith, Janakiraman Subramanian, Ramaswamy Govindan, Runjun D Kumar, Ron Bose, Li Ding & Timothy J Ley

  4. Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, USA

    Ron Bose, Timothy J Ley, Elaine R Mardis & Richard K Wilson

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  1. Malachi Griffith
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Contributions

O.L.G. and M.G. wrote the manuscript, were responsible for the selection and manual curation of data sources, creation of importers, initial design of the web interface, testing, analysis and figure creation for the manuscript. I.D. and J.F.M. helped create figures. A.C.C. and J.V.W. conceived and lead the Ruby implementation of the web interface, database, importers and application programming interface (API). J.K., M.G., O.L.G., S.M.S., I.D. and J.F.M. made contributions to the code. J.F.M. was the lead user experience web developer. S.M.S., J.M.E., J.R.W. and D.J.D. supervised software development. M.B.C. facilitated the public deployment of DGIdb and all related systems requirements. R.B., R.D.K., C.A.M. and D.E.L. provided beta testing feedback. J.S. and R.G. provided and curated the 'targeted agents in lung cancer' data set. R.B. and R.D.K. contributed the dGene data set and the breast cancer data used for analysis demonstration purposes. N.C.S. contributed manual curation of data sources and documentation. S.M.S., J.M.E., D.J.D., L.D., T.J.L., E.R.M. and R.K.W. contributed ideas and use case requirements. A.C.C., J.V.W., C.A.M., R.D.K., R.B., D.E.L. and E.R.M. contributed text and revised the manuscript. E.R.M. and R.K.W. are mentors of M.G. and O.L.G.

Corresponding authors

Correspondence to Malachi Griffith or Obi L Griffith.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Tables 1–4 (PDF 7218 kb)

Supplementary Table 5

Breast cancer druggable candidates. (XLSX 51 kb)

Supplementary Table 6

Breast cancer known druggability by patient. (XLSX 1114 kb)

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Griffith, M., Griffith, O., Coffman, A. et al. DGIdb: mining the druggable genome. Nat Methods 10, 1209–1210 (2013). https://doi.org/10.1038/nmeth.2689

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