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E-GEOD-25341 - Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Status
Released on 15 November 2010, last updated on 3 April 2013
Organism
Homo sapiens
Samples (16)
Protocols (3)
Description
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
Experiment type
ChIP-seq 
Contacts
Jacob F Degner <jdegner@uchicago.edu>, Athma A Pai, Daniel Gaffney, Jonathan K Pritchard, Roger Pique-Regi, Yoav Gilad
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-25341.idf.txt
Sample and data relationshipE-GEOD-25341.sdrf.txt
Processed data (16)Click to browse processed data
Additional data (1)E-GEOD-25341.additional.1.zip
Links