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Science 26 November 2004:
Vol. 306. no. 5701, pp. 1555 - 1558
DOI: 10.1126/science.1099511
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Reports

A Probabilistic Functional Network of Yeast Genes

Insuk Lee,1 Shailesh V. Date,1* Alex T. Adai,1{dagger} Edward M. Marcotte1,2{ddagger}

A conceptual framework for integrating diverse functional genomics data was developed by reinterpreting experiments to provide numerical likelihoods that genes are functionally linked. This allows direct comparison and integration of different classes of data. The resulting probabilistic gene network estimates the functional coupling between genes. Within this framework, we reconstructed an extensive, high-quality functional gene network for Saccharomyces cerevisiae, consisting of 4681 (~81%) of the known yeast genes linked by ~34,000 probabilistic linkages comparable in accuracy to small-scale interaction assays. The integrated linkages distinguish true from false-positive interactions in earlier data sets; new interactions emerge from genes' network contexts, as shown for genes in chromatin modification and ribosome biogenesis.

1 Center for Systems and Synthetic Biology, Institute for Molecular Biology, University of Texas at Austin, Austin, TX 78712–1064, USA.
2 Department of Chemistry and Biochemistry, Institute for Molecular Biology, University of Texas at Austin, Austin, TX 78712–1064, USA.


* Present address: Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104, USA.

{dagger} Present address: Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California at San Francisco, San Francisco, CA 94143–2240, USA.

{ddagger} To whom correspondence should be addressed. E-mail: marcotte{at}icmb.utexas.edu

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Science. ISSN 0036-8075 (print), 1095-9203 (online)