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Systematic identification of functional orthologs based on protein network comparison.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Bandyopadhyay, Sourav Sharan, Roded Ideker, Trey
Description	Country affiliation: United States Author Affiliation: Bandyopadhyay S ( Program in Bioinformatics, University of California at San Diego, La Jolla, California 92093, USA.)
Abstract	Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying functionally related proteins that supplements sequence-based comparisons with information on conserved protein-protein interactions. First, the protein interaction networks of two species are aligned by assigning proteins to sequence homology clusters using the Inparanoid algorithm. Next, probabilistic inference is performed on the aligned networks to identify pairs of proteins, one from each species, that are likely to retain the same function based on conservation of their interacting partners. Applying this method to Drosophila melanogaster and Saccharomyces cerevisiae, we analyze 121 cases for which functional orthology assignment is ambiguous when sequence similarity is used alone. In 61 of these cases, the network supports a different protein pair than that favored by sequence comparisons. These results suggest that network analysis can be used to provide a key source of information for refining sequence-based homology searches.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
Journal	Genome Research
Issue Number	3
Volume Number	16
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2006-03-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Protein Interaction Mapping Animals Drosophila Melanogaster Genetics Models, Biological Reproducibility Of Results Saccharomyces Cerevisiae Comparative Study Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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