A literature-based method for assessing the functional coherence of a gene group.
BACKGROUND
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.
Raychaudhuri
Soumya
S
Department of Genetics, Stanford Medical Informatics, 251 Campus Drive, MSOB X-215, Stanford University, Stanford, CA 94305-5479, USA.
Altman
Russ B
RB
D000043:Abstracting and Indexing; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D016000:Cluster Analysis; D030541:Databases, Genetic; D004330:Drosophila / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods*; D051379:Mice; D009323:Natural Language Processing; D039781:PubMed; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*