TY - JOUR T1 - Modeling ChIP Sequencing In Silico with Applications A1 - Zhang, Zhengdong D. A1 - Rozowsky, Joel A1 - Snyder, Michael A1 - Chang, Joseph A1 - Gerstein, Mark Y1 - 2008/08/22 N2 - Author Summary ChIP-seq is an apt combination of chromosome immunoprecipitation and next-generation sequencing to identify transcription factor binding sites in vivo on the whole-genome scale. Since its advent, this new method has generated much excitement in the field of functional genomics. Proper computational modeling of the ChIP-seq process is needed for both data scoring and determination of adequate sequencing depth, as it provides the computational foundation for analyzing ChIP-seq data. In our study, we show the characteristics of ChIP-seq data and present in silico ChIP sequencing, a computational method to simulate the experimental outcome. On the basis of our data characterization, we observed transcription factor binding sites with excessive enrichment of sequence tags. Our simulation results reveal that both the genomic background and the binding sites are not uniform. On the basis of our simulation results, we propose a statistical procedure using the more realistic genomic background model to identify binding sites in ChIP-seq data. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 4 IS - 8 UR - https://doi.org/10.1371/journal.pcbi.1000158 SP - e1000158 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000158 ER -