Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học quốc tế cung cấp cho các bạn kiến thức về ngành y đề tài: Research ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data. | Wu et al. Theoretical Biology and Medical Modelling 2010 7 18 http content 7 1 18 THEORETICAL BIOLOGY AND MEDICAL MODELLING RESEARCH Open Access ChIP-PaM an algorithm to identify protein-DNA interaction using ChIP-Seq data Song Wu 1 Jianmin Wang2 Wei Zhao1 Stanley Pounds1 and Cheng Cheng1 Correspondence 1 Department of Biostatistics St. Jude Children s Research Hospital 262 Danny Thomas Place Memphis TN 38105 USA Full list of author information is available at the end of the article Abstract Background ChIP-Seq is a powerful tool for identifying the interaction between genomic regulators and their bound DNAs especially for locating transcription factor binding sites. However high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application. Results Here we report a new algorithm ChIP-PaM for identifying transcription factor target regions in ChIP-Seq datasets. This algorithm makes full use of a protein-DNA binding pattern by capitalizing on three lines of evidence 1 the tag count modelling at the peak position 2 pattern matching of a specific tag count distribution and 3 motif searching along the genome. A novel data-based two-step eFDR procedure is proposed to integrate the three lines of evidence to determine significantly enriched regions. Our algorithm requires no technical controls and efficiently discriminates falsely enriched regions from regions enriched by true transcription factor TF binding on the basis of ChIP-Seq data only. An analysis of real genomic data is presented to demonstrate our method. Conclusions In a comparison with other existing methods we found that our algorithm provides more accurate binding site discovery while maintaining comparable statistical power. Background Understanding of transcriptional regulation mechanisms is of fundamental importance to the study of biological processes such as development drug response and .
