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Protein function prediction using neighbor relativity in protein–protein interaction network

Paper ID Volume ID Publish Year Pages File Format Full-Text
15149 1382 2013 6 PDF Available
Title
Protein function prediction using neighbor relativity in protein–protein interaction network
Abstract

There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called “Neighbor Relativity Coefficient” (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► In this article, we try to predict protein function utilizing protein interaction network. ► A new measure of proteins relativity in the network has been defined called NRC. ► NRC combines three different network topological features. ► We propose to use different relativity coefficient for each GO function type. ► NRC has better results in protein function prediction compared with previous methods.

Keywords
Protein function prediction; Neighbor Relativity Coefficient; Path connectivity; Protein–protein interaction network
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 43, April 2013, Pages 11–16
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us