RT Journal
A1 Pique-Regi, Roger
A1 Degner, Jacob F.
A1 Pai, Athma A.
A1 Gaffney, Daniel J.
A1 Gilad, Yoav
A1 Pritchard, Jonathan K.
T1 Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
JF Genome Research 
JO Genome Research 
YR 2011 
FD March 01 
VO 21 
IS 3 
SP 447 
OP 455 
DO 10.1101/gr.112623.110 
UL http://genome.cshlp.org/content/21/3/447.abstract 
AB 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 corresponding 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 DNase I 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.