Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation

Saran Vardhanabhuti, Junwen Wang, Sridhar Hannenhalli

Research output: Contribution to journalArticle

44 Scopus citations

Abstract

Computational discovery of cis-regulatory elements remains challenging. To cope with the high false positives, evolutionary conservation is routinely used. However, conservation is only one of the attributes of cis-regulatory elements and is neither necessary nor sufficient. Here, we assess two additional attributes - positional and inter-motif distance specificity - that are critical for interactions between transcription factors. We first show that for a greater than expected fraction of known motifs, the genes that contain the motifs in their promoters in a position-specific or distancespecific manner are related, both in function and/or in expression pattern. We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs.

Original languageEnglish (US)
Pages (from-to)3203-3213
Number of pages11
JournalNucleic acids research
Volume35
Issue number10
DOIs
StatePublished - May 2007

ASJC Scopus subject areas

  • Genetics

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