DGIdb - Mining the druggable genome

Griffith, Malachi; Griffith, Obi L.; Coffman, Adam C.; Weible, James V.; McMichael, Josh F; Spies, Nicholas C.; Koval, James; Das, Indraniel; Callaway, Matthew B.; Eldred, James M.; Miller, Christopher A; Subramanian, Janakiraman; Govindan, Ramaswamy; Kumar, Runjun D.; Bose, Ron; Ding, Li; Walker, Jason R.; Larson, David E.; Dooling, David J.; Smith, Scott M.; Ley, Timothy J; Mardis, Elaine R.; Wilson, Richard K.

doi:10.1038/nmeth.2689

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DGIdb - Mining the druggable genome

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Author(s): Malachi Griffith ¹ ^, ² ^, , Obi L. Griffith ¹ ^, ³ ^, , Adam C. Coffman ¹ , James V. Weible ¹ , Josh F. McMichael ¹ , Nicholas C. Spies ¹ , James Koval ¹ , Indraniel Das ¹ , Matthew B. Callaway ¹ , James M. Eldred ¹ , Christopher A. Miller ¹ , Janakiraman Subramanian ³ , Ramaswamy Govindan ³ , Runjun D. Kumar ³ , Ron Bose ³ ^, ⁴ , Li Ding ¹ ^, ² ^, ³ , Jason R. Walker ¹ , David E. Larson ¹ ^, ² , David J. Dooling ¹ , Scott M. Smith ¹ , Timothy J. Ley ¹ ^, ³ ^, ⁴ , Elaine R. Mardis ¹ ^, ² ^, ⁴ , Richard K. Wilson ¹ ^, ² ^, ⁴

Publication date (Electronic): 13 October 2013

Journal: Nature methods

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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 dgidb.org.

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Most cited references 20

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Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

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The protein kinase complement of the human genome.

G. Manning (2002)

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.

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Ensembl 2011

Paul Flicek, M. Amode, Daniel Barrell … (2010)

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

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Author and article information

Contributors

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

David E. Larson

David J. Dooling

Scott M. Smith

Timothy J. Ley

Elaine R. Mardis

Richard K. Wilson

Journal

Journal ID (nlm-journal-id): 101215604

Journal ID (pubmed-jr-id): 32338

Journal ID (nlm-ta): Nat Methods

Journal ID (iso-abbrev): Nat. Methods

Title: Nature methods

ISSN (Print): 1548-7091

ISSN (Electronic): 1548-7105

Publication date Nihms-submitted: 9 November 2013

Publication date (Electronic): 13 October 2013

Publication date (Print): December 2013

Publication date PMC-release: 01 June 2014

Volume: 10

Issue: 12

Electronic Location Identifier: 10.1038/nmeth.2689

Affiliations

[1 ]The Genome Institute, Washington University School of Medicine, St. Louis, MO

[2 ]Department of Genetics, Washington University School of Medicine, St. Louis, MO

[3 ]Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO

[4 ]Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO

Author notes

[*]

These authors contributed equally to this work.

Article

Manuscript ID: NIHMS525199

DOI: 10.1038/nmeth.2689

PMC ID: 3851581

PubMed ID: 24122041

SO-VID: aa2cded4-40bb-4d59-9fbc-cfa7f1e38580

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Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

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Funding

Funded by: National Human Genome Research Institute : NHGRI

Award ID: U54 HG003079 || HG

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DGIdb - Mining the druggable genome

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Genome Integrity

Most cited references 20

Gene Ontology: tool for the unification of biology

The protein kinase complement of the human genome.

Ensembl 2011

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