Bioinformatics Advance Access originally published online on November 10, 2006
Bioinformatics 2007 23(2):215-221; doi:10.1093/bioinformatics/btl569
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CGI: a new approach for prioritizing genes by combining gene expression and protein–protein interaction data
1 Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California Los Angeles, CA 90089-2910, USA
2 Department of Computer Science, University of Southern California Los Angeles, CA 90089-2910, USA
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Identifying candidate genes associated with a given phenotype or trait is an important problem in biological and biomedical studies. Prioritizing genes based on the accumulated information from several data sources is of fundamental importance. Several integrative methods have been developed when a set of candidate genes for the phenotype is available. However, how to prioritize genes for phenotypes when no candidates are available is still a challenging problem.
Results: We develop a new method for prioritizing genes associated with a phenotype by Combining Gene expression and protein Interaction data (CGI). The method is applied to yeast gene expression data sets in combination with protein interaction data sets of varying reliability. We found that our method outperforms the intuitive prioritizing method of using either gene expression data or protein interaction data only and a recent gene ranking algorithm GeneRank. We then apply our method to prioritize genes for Alzheimer's disease.
Availability: The code in this paper is available upon request.
Contact: fsun{at}usc.edu
Supplementary data: Supplementary data are available at Bioinformatics online.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
¶Present address: Harvard-Partners Center for Genetics and Genomics, 77 Avenue Louis Pasteur Boston, MA 02115, USA
Received on July 7, 2006; revised on October 23, 2006; accepted on November 3, 2006
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