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Science 306 (5705): 2246-2249

Copyright © 2004 by the American Association for the Advancement of Science

Use of Logic Relationships to Decipher Protein Network Organization

Peter M. Bowers,1,2 Shawn J. Cokus,3 David Eisenberg,1,2 Todd O. Yeates2,4*

Abstract: A major focus of genome research is to decipher the networks of molecular interactions that underlie cellular function. We describe a computational approach for identifying detailed relationships between proteins on the basis of genomic data. Logic analysis of phylogenetic profiles identifies triplets of proteins whose presence or absence obey certain logic relationships. For example, protein C may be present in a genome only if proteins A and B are both present. The method reveals many previously unidentified higher order relationships. These relationships illustrate the complexities that arise in cellular networks because of branching and alternate pathways, and they also facilitate assignment of cellular functions to uncharacterized proteins.

1 Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
2 Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
3 Department of Mathematics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
4 Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.

* To whom correspondence should be addressed. E-mail: yeates{at}

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