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Bioinformatics Vol. 19 no. 3 2003
Pages 396-401
© 2003 Oxford University Press

A literature-based method for assessing the functional coherence of a gene group

Soumya Raychaudhuri and Russ B. Altman *

Department of Genetics, Stanford Medical Informatics, 251 Campus Drive, MSOB X-215, Stanford University, Stanford, CA 94305-5479, USA

Received on July 25, 2002 ; revised on September 23, 2002 ; accepted on September 28, 2002

Motivation: Many experimental and algorithmic approaches in biology generate groups of genes that need to be examined for related functional properties. For example, gene expression profiles are frequently organized into clusters of genes that may share functional properties. We evaluate a method, neighbor divergence per gene (NDPG), that uses scientific literature to assess whether a group of genes are functionally related. The method requires only a corpus of documents and an index connecting the documents to genes.

Results: We evaluate NDPG on 2796 functional groups generated by the Gene Ontology consortium in four organisms: mouse, fly, worm and yeast. NDPG finds functional coherence in 96, 92, 82 and 45% of the groups (at 99.9% specificity) in yeast, mouse, fly and worm respectively.

Availability: Contact authors.

Contact: russ.altman{at}stanford.edu

* To whom correspondence should be addressed.


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