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This article is part of the supplement: The 2009 International Conference on Bioinformatics & Computational Biology (BioComp 2009)

Open Access Research

Identifying functional relationships within sets of co-expressed genes by combining upstream regulatory motif analysis and gene expression information

Viktor Martyanov and Robert H Gross*

Author Affiliations

Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA

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BMC Genomics 2010, 11(Suppl 2):S8  doi:10.1186/1471-2164-11-S2-S8

Published: 2 November 2010



Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to generate functionally coherent and biologically meaningful subclusters of genes. Specifically, the approach clusters co-expressed genes on the basis of similar content and distributions of predicted statistically significant sequence motifs in their upstream regions.


We applied our method to several sets of co-expressed genes and were able to define subsets with enrichment in particular biological processes and specific upstream regulatory motifs.


These results show the potential of our technique for functional prediction and regulatory motif identification from microarray data.