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Semantically predicting protein functions based on protein functional connectivity

Paper ID Volume ID Publish Year Pages File Format Full-Text
15109 1378 2013 6 PDF Available
Title
Semantically predicting protein functions based on protein functional connectivity
Abstract

BackgroundThe current availability of public protein–protein interaction (PPI) databases which are usually modelled as PPI networks has led to the rapid development of protein function prediction approaches. The existing network-based prediction approaches mainly focus on the topological similarities between immediately interacting proteins, neglecting the protein functional connectivity which is the functional tightness between proteins. In this paper, we attempt to predict the functions of unannotated proteins based on PPI networks by incorporating the protein functional connectivity, as well as the similarity of protein functions, into the prediction procedure.ResultsAn approach named Semantic protein function Prediction based on protein Functional Connectivity (SPFC) is proposed to achieve a higher accuracy in predicting functions of unannotated protein. We define the functional connectivity and function addition for each protein, and incorporate them into the prediction. We evaluated the SPFC on real PPI datasets and the experiment results show that the SPFC method is more effective in function prediction than other network-based approaches.ConclusionIncorporating the functional connectivity of each protein into the function prediction can significantly improve the accuracy of protein prediction.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► We defined functional connectivity in protein–protein interaction network to measure the semantic relationships between proteins and its neighbours. ► We defined function addition to measure the strength of a function correlating with other functions in a protein. ► We integrate functional connectivity and function addition to effectively predict protein functions.

Keywords
Protein function; Function prediction; Functional connectivity
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Semantically predicting protein functions based on protein functional connectivity
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 44, June 2013, Pages 9–14
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