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).
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.
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.
ENCODE tracks typically contain one or more of the following views:
- Peaks
- Regions of signal enrichment based on processed data
(normalized data from pooled replicates). 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.
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 bp) 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 less than or equal to 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 less than or equal to 0.05 are considered to be
significantly enriched compared to the input DNA control.
Release Notes
This is Release 3 (August 2012). This release adds in 37 new experiments including 1 new cell line and 7 new antibodies.
Credits
These data were generated and analyzed by the labs of
Michael Snyder at Stanford University;
Mark Gerstein and
Sherman Weissman at Yale University;
Peggy Farnham at University of Southern California; and
Kevin Struhl at Harvard.
Contact:
Philip Cayting.
References
Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ.
Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome.
J Biol Chem. 2011 Apr 8;286(14):11985-96.
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.
Iyengar S, Ivanov AV, Jin VX, Rauscher FJ 3rd, Farnham PJ.
Functional analysis of KAP1 genomic recruitment.
Mol Cell Biol. 2011 May;31(9):1833-47.
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.
Publications
Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH.
Autophagy driven by a master regulator of hematopoiesis.
Mol Cell Biol. 2012 Jan;32(1):226-39.
Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L.
SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers.
Mol Cell. 2011 Nov 4;44(3):410-23.
Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH.
Genetic framework for GATA factor function in vascular biology.
Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6.
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.