a chip-seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding siteschip-seq基准显示序列保护主要提高了检测强劲的转录因子结合位点.pdfVIP

A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites ˚ 1 1 1 ˚ 1,2 Tony Handstad , Morten Beck Rye , Finn Drabløs , Pal Sætrom * 1 Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway, 2 Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway Abstract Background: Transcription factors are important controllers of gene expression and mapping transcription factor binding sites (TFBS) is key to inferring transcription factor regulatory networks. Several methods for predicting TFBS exist, but there are no standard genome-wide datasets on which to assess the performance of these prediction methods. Also, it is believed that information about sequence conservation across different genomes can generally improve accuracy of motif-based predictors, but it is not clear under what circumstances use of conservation is most beneficial. Results: Here we use published ChIP-seq data and an improved peak detection method to create comprehensive benchmark datasets for prediction methods which use known descriptors or binding motifs to detect TFBS in genomic sequences. We use this benchmark to assess the performance of five different prediction methods and find that the methods that use information about sequence conservation generally perform better than simpler motif-scanning methods. The difference is greater on high-affinity peaks and when using short and information-poor motifs. However, if the motifs are specific and information-rich, we find that simple motif-scanni