Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.
E-GEOD-25341 - Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
Released on 15 November 2010, last updated on 3 April 2013
Accurate functional annotation of regulatory elements is essential for understanding global gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites correspond-ing to 239 position weight matrices of known transcription factor binding motifs, and 49 novel sequence motifs. To generate this map, we developed a probabilistic framework that integrates cell- or tissue-speciﬁc experimental data such as histone modiﬁcations and DNa-seI cleavage patterns with genomic information such as gene annotation and evolutionary conservation. Comparison to empirical ChIP-seq data suggests that our method is highly accurate yet has the advantage of targeting many factors in a single assay. We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell-types or tissues under diverse conditions. DNaseI-Seq on two YRI Hapmap cell lines. Each individual sequenced on 8 lanes of the Illumina Genome Analyzer II
Jacob F Degner <email@example.com>, Athma A Pai, Daniel Gaffney, Jonathan K Pritchard, Roger Pique-Regi, Yoav Gilad
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. , PMID:21106904