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This article is part of the supplement: Proceedings of the Sixth Annual MCBIOS Conference. Transformational Bioinformatics: Delivering Value from Genomes

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Integrating phenotype and gene expression data for predicting gene function

Brandon M Malone12*, Andy D Perkins12 and Susan M Bridges12

Author Affiliations

1 Department of Computer Science and Engineering, Box 9637, Mississippi State University, Mississippi State, MS, 39762 USA

2 Institute for Digital Biology, Mississippi State University, Mississippi State, MS, 39762 USA

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BMC Bioinformatics 2009, 10(Suppl 11):S20  doi:10.1186/1471-2105-10-S11-S20

Published: 8 October 2009



This paper presents a framework for integrating disparate data sets to predict gene function. The algorithm constructs a graph, called an integrated similarity graph, by computing similarities based upon both gene expression and textual phenotype data. This integrated graph is then used to make predictions about whether individual genes should be assigned a particular annotation from the Gene Ontology.


A combined graph was generated from publicly-available gene expression data and phenotypic information from Saccharomyces cerevisiae. This graph was used to assign annotations to genes, as were graphs constructed from gene expression data and textual phenotype information alone. While the F-measure appeared similar for all three methods, annotations based upon the integrated similarity graph exhibited a better overall precision than gene expression or phenotype information alone can generate. The integrated approach was also able to assign almost as many annotations as the gene expression method alone, and generated significantly more total and correct assignments than the phenotype information could provide.


These results suggest that augmenting standard gene expression data sets with publicly-available textual phenotype data can help generate more precise functional annotation predictions while mitigating the weaknesses of a standard textual phenotype approach.