Detecting DNA regulatory motifs by incorporating positional trendsin information content

Journal Article · Tue May 04 00:00:00 EDT 2004 · Genome Biology

DOI:https://doi.org/10.1186/gb-2004-5-7-r50· OSTI ID:861584

Kechris, Katherina J; van Zwet, Erik; Bickel, Peter J; Eisen, Michael B

On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE. Office of Management Budget and Evaluation; NationalInstitutes of Health Grant R01 HG002779-02, National Science FoundationGraduate Research Fellowship
• DOE Contract Number: DE-AC02-05CH11231
• OSTI ID: 861584
• Report Number(s): LBNL-55737; R&D Project: GHEIS2; BnR: 400412000; TRN: US200601%%54
• Journal Information: Genome Biology, Vol. 5, Issue 7; Related Information: Journal Publication Date: 06/24/2004
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
DNA
TRANSCRIPTION FACTORS
MATHEMATICAL MODELS
POSITIONING