Description
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).
Each experiment is associated with an input signal, which represents the
control condition where immunoprecipitation with non-specific immunoglobulin
was performed in the same cell type. 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, as identified by the PeakSeq algorithm (Peaks).
The sequence reads, quality scores, and alignment coordinates from
these experiments are available for download.
Display Conventions and Configuration
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.
This track contains the following views:
- Peaks
- Regions of signal enrichment based on processed data
(normalized data from pooled replicates). Intensity is represented in
grayscale, the darker shading shows higher intensity (a solid vertical line
in the peak region represents the the point with the highest signal).
ENCODE Peaks tables contain fields for statistical significance,
including the minimum false discovery rate (FDR) threshold at which the test may be called significant
(qValue).
- Signal
- Density graph (wiggle) of signal enrichment based on
processed data.
Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.
Methods
Cells were grown according to the approved
ENCODE cell culture protocols.
For details on the chromatin immunoprecipitation protocol used,
see (Euskirchen et al., 2007), (Rozowsky et al., 2009)
and (Auerbach 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. Reads were pooled from
all submitted replicates to generate the Peak and Signal files. Per-replicate
aligments and sequences are available for download at
downloads page.
For each 1 Mb segment of each chromosome, a peak height threshold was determined
by requiring a false discovery rate <= 0.01 when comparing the number of peaks
above said threshold to the number of peaks 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 ≤ 0.01 are considered to be significantly
enriched compared to the input DNA control.
Release Notes
This is Release 4 (August 2012). It contains a total of 88 ChIP-seq experiments on transcriptions factor binding with the addition of 22 new
experiments including 12 new antibodies.
Previous versions of files are available for download from the
FTP site.
Credits
These data were generated and analyzed by the labs of
Michael Snyder at Stanford University and
Sherman Weissman at Yale University.
Contact: Philip Cayting.
References
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M.
Mapping accessible chromatin regions using Sono-Seq.
Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31.
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 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.