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

Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Motivation: 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. Results: 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.

Original languageEnglish (US)
Pages (from-to)2473-2477
Number of pages5
JournalBioinformatics
Volume25
Issue number19
DOIs
StatePublished - 2009

Fingerprint

Transcription factors
Drosophilidae
Binding sites
Transcription Factor
Drosophila melanogaster
Sharing
Transcription Factors
Genes
Binding Sites
Gene
Gene Expression
Genomics
Reverse
Relationships
Molecular Sequence Annotation
Functional Genomics
Biological Phenomena
Comparative Genomics
Common factor
Semantic Similarity

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. / Marco, Antonio; Konikoff, Charlotte; Karr, Timothy L.; Kumar, Sudhir.

In: Bioinformatics, Vol. 25, No. 19, 2009, p. 2473-2477.

Research output: Contribution to journalArticle

Marco, Antonio ; Konikoff, Charlotte ; Karr, Timothy L. ; Kumar, Sudhir. / Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. In: Bioinformatics. 2009 ; Vol. 25, No. 19. pp. 2473-2477.
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