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Chem Biol. 2013 May 23;20(5):629-35. doi: 10.1016/j.chembiol.2013.03.018.

Pathway databases: making chemical and biological sense of the genomic data flood.

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1
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, MSB 390, New York, NY 10016, USA. deustp01@med.nyu.edu

Abstract

Pathway databases are a means to systematically associate proteins with their functions and link them into networks that describe the reaction space of an organism. Here, the Reactome Knowledgebase provides a convenient example to illustrate strategies used to assemble such a reaction space based on manually curated experimental data, approaches to semiautomated extension of these manual annotations to infer annotations for a large fraction of a species' proteins, and the use of networks of functional annotations to infer pathway relationships among variant proteins that have been associated with disease risk through genome-wide surveys and resequencing studies of tumors.

PMID:
23706629
PMCID:
PMC3678733
DOI:
10.1016/j.chembiol.2013.03.018
[Indexed for MEDLINE]
Free PMC Article
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