Network Analysis Reveals New Players

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Science's STKE  07 Oct 2003:
Vol. 2003, Issue 203, pp. tw387-TW387
DOI: 10.1126/stke.2003.203.tw387

Kelley et al. used data from the Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu/) and developed a computational method, which they call PathBlast (http://www.pathblast.org/bioc/pathblast/blastpathway.jsp), to analyze networks of interacting proteins. Using this approach, they aligned functionally similar pathways in Saccharomyces cerevisiae and Helicobacter pylori. This allowed gaps in the pathways to be identified and allowed proteins with unknown functions to be tentatively assigned to functional pathways; these results can direct future wet laboratory research. In addition, the analysis showed potential intersections between cellular pathways and potential new functions for components. Using their pathway query process, the authors searched within the yeast network to identify pathways involved in similar functions (paralogous pathways), which led to the identification of putative new pathways and partners within pathways, such as the ubiquitin conjugation process, the SUMO conjugation process, and the mitogen-activated protein kinase pathway. Thus, network analysis provides new directions for the wet laboratory and provides validation of biological relevance based on the conservation of pathways among multiple species.

B. P. Kelley, R. Sharan, R. M. Karp, T. Sittler, D. E. Root, B. R. Stockwell, T. Ideker, Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. U.S.A. 100, 11394-11399 (2003). [Abstract] [Full Text]

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