ENC TF Binding Super-track Settings
 
ENCODE Transcription Factor Binding Tracks   (All Regulation tracks)

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Uniform TFBS  Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis  ENCODE March 2012 Freeze
HAIB TFBS  Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB
SYDH TFBS  Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
UChicago TFBS  Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago
UTA TFBS  Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin)  ENCODE July 2011 Freeze
UW CTCF Binding  CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington

wgEncodeTfBindingSuper.html

Description

Transcription is regulated through the binding of transcription factor proteins to specific cis-level regulatory sites in the DNA. The nature of this regulation depends on the transcription factor. For example, some proteins activate transcription by recruiting RNA polymerase, some repress transcription by suppressing this recruitment, and others insulate proximal regions from the activity of nearby transcriptional activators or repressors. A key characteristic of each transcription factor protein is its DNA binding domain. Each DNA binding domain recognizes and interacts with DNA that matches a specific nucleotide pattern, or motif. These motifs tend to be short and degenerate, so even when the DNA binding motif is known, one cannot generally predict where a given transcription factor may bind. In general, transcription factor binding is determined experimentally.

These tracks contain transcription factor binding sites determined by ChIP-seq. This process involves fragmenting DNA, selecting the fragments of DNA that are bound by a certain transcription factor, and sequencing those DNA fragments. This generally yields a large library of DNA sequences, including some that were bound by the transcription factor directly, some that were bound indirectly via interactions with other molecules, and some false positives (such as cases of nonspecific binding). With the appropriate analysis methods, ChIP-seq can be a valuable approach for elucidating transcription factor binding and cis-level regulation.

Display Conventions

These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages.

Credits


These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks.

References

Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909.

Hudson ME, Snyder M. High-throughput methods of regulatory element discovery. Biotechniques. 2006 Dec;41(6):673, 675, 677 passim.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.