asap a framework for over-representation statistics for transcription factor binding sites尽快的框架代表统计数据转录因子结合位点.pdf

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites 1 1 1 1 1 2 Troels T. Marstrand *, Jes Frellsen , Ida Moltke , Martin Thiim , Eivind Valen , Dorota Retelska , Anders Krogh1 1 Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark, 2 Swiss Institute of Bioinformatics, Swiss Institute for Experimental Cancer Research (ISREC), Epalinges, Switzerland Abstract Background: In studies of gene regulation the efficient computational detection of over-represented transcription factor binding sites is an increasingly important aspect. Several published methods can be used for testing whether a set of hypothesised co-regulated genes share a common regulatory regime based on the occurrence of the modelled transcription factor binding sites. However there is little or no information available for guiding the end users choice of method. Furthermore it would be necessary to obtain several different software programs from various sources to make a well-founded choice. Methodology: We introduce a software package, Asap, for fast searching with position weight matrices that include several standard methods for assessing over-representation. We have compared the ability of these methods to detect over- represented transcription factor binding sites in artificial promoter sequences. Controlling all aspects of our input data we are able to identify the optimal statistics across multiple threshold values and for sequence sets containing different distributions of transcription factor binding sites.