Integration of Genome and Epigenetic Feature to Predict c-Myc Targets

Yili Chen
Delaware Biotechnology Institute; University of Delaware


Abstract

c-Myc is an important oncogene and is one of the transcription factors whose binding and regulation activity are affected by local epigenetic status of target DNA, such as DNA methylation, chromatin acetylation. But like other such transcription factors, the local epigenetic status is largely ignored in computational analysis of c-Myc targets. In this talk, I will first present a computational model to predict local DNA methylation status based on DNA sequence. The DNA methylation prediction is then integrated with chromatin acetylation data and other sequence information to predict high affinity c-Myc binding sites in the human genome. Finally, the predicted c-Myc binding sites, microarray data from various cancers and gene ontology data are combined to predict c-Myc targets. The predictions are validated with multiple published experimental studies and hundreds of new targets are also suggested.