Initial Results In Using de Novo Motif Inference to Detect Cis-Regulatory Modules

Authors:
Jeffrey A. Thompson;Clare Bates Congdon
Affiliations:
University of Southern Maine, Portland, Maine 04104, USA;University of Southern Maine, Portland, Maine 04104, USA
Venue:
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Year:
2013

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An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

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Abstract

In this work, we extend GAMI, a de novo motif inference system, to find sets of motifs that may function as part of a cis-regulatory module (CRM). Evidence suggests that most transcription factors in humans are part of a CRM, so this approach is expected to yield stronger candidates for de novo inference of candidate regulatory elements.