Spectral affinity in protein networks.

BMC Systems Biology
Konstantin VoevodskiYu Xia

Abstract

Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at pred...Continue Reading

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Citations

Mar 14, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Aleksandar Stojmirović, Yi-Kuo Yu
Jun 13, 2012·Bioinformatics·Yu-Keng Shih, Srinivasan Parthasarathy
Apr 19, 2013·Bioinformatics·Lieven P C VerbekeKathleen Marchal
Feb 26, 2014·BMC Systems Biology·Florian Goebels, Dmitrij Frishman
May 17, 2012·BMC Research Notes·Aleksandar StojmirovićYi-Kuo Yu
Jul 20, 2010·Journal of Proteomics·Peggy I Wang, Edward M Marcotte
Apr 23, 2013·Journal of Bioinformatics and Computational Biology·Sriganesh Srihari, Hon Wai Leong
Jun 14, 2017·Nature Reviews. Genetics·Lenore CowenRoded Sharan
Aug 4, 2017··Jure LeskovecDavid F. Gleich

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Methods Mentioned

BETA
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Software Mentioned

Western
Two
AC
ApproximatePR
MS

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