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Combining gene expression profiles and protein–protein interaction data to infer gene functions

Paper ID Volume ID Publish Year Pages File Format Full-Text
25709 43593 2006 11 PDF Available
Title
Combining gene expression profiles and protein–protein interaction data to infer gene functions
Abstract

The ever-increasing flow of gene expression profiles and protein–protein interactions has catalyzed many computational approaches for inference of gene functions. Despite all the efforts, there is still room for improvement, for the information enriched in each biological data source has not been exploited to its fullness. A composite method is proposed for classifying unannotated genes based on expression data and protein–protein interaction (PPI) data, which extracts information from both data sources in novel ways. With the noise nature of expression data taken into consideration, importance is attached to the consensus expression patterns of gene classes instead of the actual expression profiles of individual genes, thus characterizing the composite method with enhanced robustness against microarray data variation. With regard to the PPI network, the traditional clear-cut binary attitude towards inter- and intra-functional interactions is abandoned, whereas a more objective perspective into the PPI network structure is formed through incorporating the varied function–function interaction probabilities into the algorithm. The composite method was implemented in two numerical experiments, where its improvement over single-data-source based methods was observed and the superiority of the novel data handling operations was discussed.

Keywords
Gene function prediction; Gene expression; Protein–protein interaction; Simulated annealing
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Combining gene expression profiles and protein–protein interaction data to infer gene functions
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 124, Issue 3, 25 July 2006, Pages 475–485
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