Bioinformatics Advance Access originally published online on December 17, 2004
Bioinformatics 2005 21(4):423-429; doi:10.1093/bioinformatics/bti186
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Bioinformatics vol. 21 issue 4 © Oxford University Press 2005; all rights reserved.
Clustering of diverse genomic data using information fusion
Department of Computer Science and Engineering, Pennsylvania State University University Park, PA 16802, USA
*To whom correspondence should be addressed.
Motivation: Genome sequencing projects and high-through-put technologies like DNA and Protein arrays have resulted in a very large amount of information-rich data. Microarray experimental data are a valuable, but limited source for inferring gene regulation mechanisms on a genomic scale. Additional information such as promoter sequences of genes/DNA binding motifs, gene ontologies, and location data, when combined with gene expression analysis can increase the statistical significance of the finding. This paper introduces a machine learning approach to information fusion for combining heterogeneous genomic data. The algorithm uses an unsupervised joint learning mechanism that identifies clusters of genes using the combined data.
Results: The correlation between gene expression time-series patterns obtained from different experimental conditions and the presence of several distinct and repeated motifs in their upstream sequences is examined here using publicly available yeast cell-cycle data. The results show that the combined learning approach taken here identifies correlated genes effectively. The algorithm provides an automated clustering method, but allows the user to specify apriori the influence of each data type on the final clustering using probabilities.
Availability: Software code is available by request from the first author.
Contact: jkasturi{at}cse.psu.edu