de-novo discovery of differentially abundant transcription factor binding sites including their positional preference新创的发现不同的丰富的转录因子结合位点包括位置偏好.pdfVIP

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference 1. 2. 3,4 2 1 2 Jens Keilwagen *, Jan Grau , Ivan A. Paponov , Stefan Posch , Marc Strickert , Ivo Grosse 1 Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany, 2 Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany, 3 Institute of Biology II/Botany, Faculty of Biology, Albert–Ludwigs–University Freiburg, Freiburg, Germany, 4 Centre for Biological Signalling Studies (BIOSS), Albert–Ludwigs–University of Freiburg, Freiburg, Germany Abstract Transcription factors are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in promoters. The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant transcription factor binding sites that models existing positional preferences of binding sites and adjusts the length of the motif in the learning process. Evaluating Dispom, we find that its prediction performance is superior to existing tools for de-novo motif discovery for 18 benchmark data sets with planted binding sites, and for a metazoan compendium based on experimental data from micro- array, ChIP-chip, ChIP-DSL, and DamID as well as Gene Ontology data. Finally, we apply Dispom to find binding sites differentially abundant in promoters of auxin-responsive genes extracted from Arabidopsis thalia