A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data.

ABSTRACT: Understanding gene regulation is a key challenge in today's biology. The new technologies of protein-binding microarrays (PBMs) and high-throughput SELEX (HT-SELEX) allow measurement of the binding intensities of one transcription factor (TF) to numerous synthetic double-stranded DNA sequences in a single experiment. Recently, Jolma et al. reported the results of 547 HT-SELEX experiments covering human and mouse TFs. Because 162 of these TFs were also covered by PBM technology, for the first time, a large-scale comparison between implementations of these two in vitro technologies is possible. Here we assessed the similarities and differences between binding models, represented as position weight matrices, inferred from PBM and HT-SELEX, and also measured how well these models predict in vi

SUBMITTER: Orenstein Y 

PROVIDER: S-EPMC4005680 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature