|
| Status |
Public on Nov 15, 2010 |
| Title |
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
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.
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| |
|
| Overall design |
DNaseI-Seq on two YRI Hapmap cell lines. Each individual sequenced on 8 lanes of the Illumina Genome Analyzer II
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| |
|
| Contributor(s) |
Pique-Regi R, Degner JF, Pai AA, Gaffney D, Gilad Y, Pritchard JK |
| Citation(s) |
21106904 |
| Submission date |
Nov 15, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacob F Degner |
| E-mail(s) |
jdegner@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Pritchard
|
| Street address |
920 E. 58th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
|
| Samples (16)
|
|
| Relations |
| SRA |
SRP004446 |
| BioProject |
PRJNA134875 |
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