This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq). Included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (Signal), along with sites that have the greatest evidence of transcription factor binding (Peaks).
The sequence reads, quality scores, and alignment coordinates from these experiments are available for download.
This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. ENCODE tracks typically contain one or more of the following views:
Cells were grown according to the approved ENCODE cell culture protocols. Further preparations were similar to those previously published (Euskirchen et al., 2007) with the exceptions that the cells were unstimulated and sodium orthovanadate was omitted from the buffers. For details on the chromatin immunoprecipitation protocol used, see Euskirchen et al. (2007) and Rozowsky et al. (2009).
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.
For each 1 Mb segment of each chromosome a peak height threshold was determined by requiring a false discovery rate <= 0.05 when comparing the number of peaks above threshold as compared the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value <= 0.05 are considered to be significantly enriched compared to the input DNA control.
Expression data generated as confirmation of the TFBS data can be found in the Yale Poly-A tracks (coming soon).
This is Release 2 (Oct 2009) of this track, which includes data from additional experiments, and the changes described below.
A number of previously released datasets have been replaced by updated versions. The affected database tables and files include 'V2' (or alternatively, 'Rel2') in the name, and metadata is marked with "submittedDataVersion=V2", followed by the reason for replacement. Specific changes are:
| Peaks | The previously released "Peaks" datasets had an off-by-one start location error and did not include pValues and point peaks. All Peaks data now have these problems corrected. |
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| Signal | The majority of the previously released "Signal" datasets contained a sparse representation of the signal. These have been corrected to be the continuous signal intended. |
| Raw Signal | The previously-available "Raw Signal" view of the data is no longer provided as the 'Signals' view provides a better measure of enrichment, and algorithms for the Raw Signal are in flux. |
| K562 vs. K562b | The Farnham lab (UC Davis) K562 cell line variant differs from the Snyder (Yale) and Struhl (Harvard) labs and is now labeled: K562b. Experiments on K562b should be contrasted with Input (UCDavis). The K562 Input previously released has been replaced by two versions marked K562 and K562b. The K562 version used by the Snyder and Struhl groups directly replaces the previous version, and is versioned at V2. The K562b used by the Farnham group is now provided as K562b. |
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| HepG2 vs. HepG2b | The Farnham lab HepG2 cell line is now labeled HepG2b. Experiments on HepG2b should be contrasted with Input (UCDavis). |
These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at UC Davis; and Kevin Struhl at Harvard. Contact: datasubmission@gersteinlab.org.
Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M et al. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May;24(9):3804-14.
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.
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M et al. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52.
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-7.
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009 Jan;27(1):66-75.
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.