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Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster

Marco, A and Konikoff, C and Karr, TL and Kumar, S (2009) 'Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster.' Bioinformatics, 25 (19). pp. 2473-2477. ISSN 1367-4803

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Abstract

<h4>Motivation</h4>In functional genomics, it is frequently useful to correlate expression levels of genes to identify transcription factor binding sites (TFBS) via the presence of common sequence motifs. The underlying assumption is that co-expressed genes are more likely to contain shared TFBS and, thus, TFBS can be identified computationally. Indeed, gene pairs with a very high expression correlation show a significant excess of shared binding sites in yeast. We have tested this assumption in a more complex organism, Drosophila melanogaster, by using experimentally determined TFBS and microarray expression data. We have also examined the reverse relationship between the expression correlation and the extent of TFBS sharing.<h4>Results</h4>Pairs of genes with shared TFBS show, on average, a higher degree of co-expression than those with no common TFBS in Drosophila. However, the reverse does not hold true: gene pairs with high expression correlations do not share significantly larger numbers of TFBS. Exception to this observation exists when comparing expression of genes from the earliest stages of embryonic development. Interestingly, semantic similarity between gene annotations (Biological Process) is much better associated with TFBS sharing, as compared to the expression correlation. We discuss these results in light of reverse engineering approaches to computationally predict regulatory sequences by using comparative genomics.

Item Type: Article
Uncontrolled Keywords: Animals; Drosophila melanogaster; Transcription Factors; Oligonucleotide Array Sequence Analysis; Computational Biology; Genomics; Gene Expression; Binding Sites
Subjects: Q Science > Q Science (General)
Divisions: Faculty of Science and Health
Faculty of Science and Health > Life Sciences, School of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 23 Mar 2015 19:36
Last Modified: 18 Aug 2022 11:29
URI: http://repository.essex.ac.uk/id/eprint/8503

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