High-throughput DNA sequencing has transformed studies of the human genome, not only allowing fast and inexpensive determination of DNA sequence, but also the development of genome-scale assays that measure DNA structure and its interactions other biomolecules. We have developed an integrative method to identify patterns from multiple experiments of these kinds simultaneously while taking full advantage of high-resolution data, discovering joint patterns across different assay types. We apply this method to ENCODE chromatin data, including ChIP-seq data on covalent histone modifications and transcription factor binding, DNaseI-seq and FAIRE-seq readouts of open chromatin, and RNA-seq measurements of transcription prdoucts. In an unsupervised fashion, we identify patterns associated with transcription start sites, gene ends, enhancers, CTCF elements, and repressed regions. The method yields a model which elucidates the relationship between assay observations and functional elements in the genome.
Sunday, April 21, 2013
Free and open to the public