Explicit DNase sequence bias modeling enables high resolution transcription factor footprint detection

ABSTRACT: DNase I footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. A number of computational approaches have been developed to accurately identify DNase-seq footprints and these methods have been used as a predictor of TF-DNA interactions by itself or in combination with other epigenetic features. However, recent studies have pointed to a substantial cleavage bias of DNase and its impact on footprinting, casting doubts on its predictive performance. To assess the potential for using DNaseI to identify individual binding sites, we performed DNase-seq experiments on deproteinized naked genomic DNA isolated from

ORGANISM(S): Homo sapiens

SUBMITTER: Christopher Frank 

PROVIDER: E-GEOD-61105 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress