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Yale ChIP-chip Sites (Yale ChIP)

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*Cell_Type*
HeLaS3
GM06990
K562

*Factor*
BAF155
BAF170
c-Fos
c-Jun
TAF1
Pol2
Pol2-N
H4Kac4
H3K27me3
BAF47
STAT1
P65-C
P65-N
SMARCA4
SMARCA6
NRSF

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	dense	YU BAF155 HeLa	Yale ChIP-chip (BAF155 ab, HeLa S3 cells) Sites	schema
	dense	YU BAF170 HeLa	Yale ChIP-chip (BAF170 ab, HeLa S3 cells) Sites	schema
	dense	YU c-Fos HeLa	Yale ChIP-chip (c-Fos ab, HeLa S3 cells) Sites	schema
	dense	YU c-Jun HeLa	Yale ChIP-chip (c-Jun ab, HeLa S3 cells) Sites	schema
	dense	YU TAF1 HeLa	Yale ChIP-chip (TAF1 ab, HeLa S3 cells) Sites	schema
	dense	YU Pol2 HeLa	Yale ChIP-chip (Pol2 ab, HeLa S3 cells) Sites	schema
	dense	YU Pol2N HeLa	Yale ChIP-chip (Pol2 N-terminus ab, HeLa S3 cells) Sites	schema
	dense	YU H4Kac4 HeLa	Yale ChIP-chip (H4Kac4 ab, HeLa S3 cells) Sites	schema
	dense	YU H3K27me3 HeLa	Yale ChIP-chip (H3K27me3 ab, HeLa S3 cells) Sites	schema
	dense	YU STAT1 HeLa IF	Yale ChIP-chip (STAT1 ab, HeLa S3 cells, Interferon-alpha treated) Sites	schema
	dense	YU P65-N HeLa TNF	Yale ChIP-chip (NFKB p65 N-terminus ab, HeLa S3 cells, TNF-alpha treated) Sites	schema
	dense	YU P65-C HeLa TNF	Yale ChIP-chip (NFKB p65 C-terminus ab, HeLa S3 cells, TNF-alpha treated) Sites	schema
	dense	YU SMARCA4 HeLa	Yale ChIP-chip (SMARCA4, HeLa S3 cells) Sites	schema
	dense	YU SMARCA6 HeLa	Yale ChIP-chip (SMARCA6, HeLa S3 cells) Sites	schema
	dense	YU NRSF HeLa	Yale ChIP-chip (NRSF, HeLa S3 cells) Sites	schema
	dense	YU Pol2 GM	Yale ChIP-chip (Pol2 ab, GM06990 cells) Sites	schema
	dense	YU Pol2N GM	Yale ChIP-chip (Pol2 N-terminus ab, GM06990 cells) Sites	schema
	dense	YU H4Kac4 GM	Yale ChIP-chip (H4Kac4 ab, GM06990 cells) Sites	schema
	dense	YU BAF155 K562	Yale ChIP-chip (BAF155 ab, K562 cells) Sites	schema
	dense	YU BAF170 K562	Yale ChIP-chip (BAF170 ab, K562 cells) Sites	schema
	dense	YU BAF47 K562	Yale ChIP-chip (BAF47 ab, K562 cells) Sites	schema

Data version: ENCODE Oct 2005 Freeze
Data coordinates converted via liftOver from: May 2004 (NCBI35/hg17)

Description

This track shows the map of -log10(P-value) of binding sites (as determined in the Methods below) for ChIP-chip using DNA from immunoprecipitated chromatin from either human HelaS3 (cervix epithelial adenocarcinoma), GM06990 (lymphoblastoid) or K562 (myeloid leukemia-derived) cells hybridized to maskless photolithographic arrays. The arrays consist of 50-mer oligonucleotides tiled with 12-nt overlaps covering most of the non-repetitive DNA sequence of the ENCODE regions. Chromatin immunoprecipitation was carried out for each experiment using antibodies against the following targets: BAF155, BAF170, INI1/BAF47, c-Fos, c-Jun, TAF1/TAFII250, RNA polymerase II, histone H4 tetra-acetylated lysine (H4Kac4), histone H3 tri-methylated lysine (H3K27me3), STAT1, nuclear factor kappa B (NFKB) p65, SMARCA4/BRG1, SMARCA6 and NRSF. Additionally, HeLa S3 cells immunoprecipitated with STAT1 were pre-treated with interferon-alpha and HeLa S3 cells immunoprecipitated with NFKB antibody were pre-treated with tumor necrosis factor-alpha (TNF-alpha) (see table below).

This track shows the combined results of three or four multiple biological replicates. For all arrays, the ChIP DNA was labeled with Cy5 and the control DNA was labeled with Cy3. These data are available at NCBI GEO (see table below for links), which also provides additional information about the experimental protocols.

Target	GEO Accession(s)	Description
BAF155 (H-76)	GSE3549 (HeLa S3 cells) and GSE6898 (K562 cells)	BAF155 (Brg1-Associated Factor, 155 kD) is a human homolog of yeast SWI3. The Swi-Snf chromatin-remodeling complex was first described in yeast, and similar proteins have been found in mammalian cells. The human Swi-Snf complex is comprised of at least nine polypeptides, including two ATPase subunits, Brm and Brg-1. Other members of the human Swi-Snf complex are termed BAFs for Brg1-associated factors. BAF155 is a conserved (core) component that stimulates the chromatin remodeling activity of Brg1.
BAF170 (H-116)	GSE3550 (HeLa S3 cells) and GSE6896 (K562 cells)	BAF170 (Brg1-Associated Factor, 170 kD) is a human homolog of yeast SWI3, a protein important in chromatin remodeling. It is a conserved (core) component of the Swi-Snf complex that stimulates the chromatin remodeling activity of Brg1 (see the description for BAF155).
INI1/BAF47 (H-300)	GSE6897 (K562 cells)	INI1 (Integrase Interactor 1) or BAF47 is a human homolog of yeast SNF5, a protein important in chromatin remodeling.
c-Fos	GSE3449 (HeLa S3 cells)	c-Fos (transcription factor) is the cellular homolog of the v-fos viral oncogene. It is a member of the leucine zipper protein family and its transcriptional activity has been implicated in cell growth, differentiation, and development. Fos is induced by many stimuli, ranging from mitogens to pharmacological agents. c-Fos has been shown to be associated with another proto-oncogene, c-Jun, and together they bind to the AP-1 binding site to regulate gene transcription. Like CREB, c-Fos is regulated by p90Rsk.
c-Jun	GSE3448 (HeLa S3 cells)	c-Jun (transcription factor), also known as AP-1 (activator protein 1), is the cellular homolog of the avian sarcoma virus oncogene v-jun, and as such can be referred to as a proto-oncogene.
TAF1/TAFII250	GSE3450 (HeLa S3 cells)	TAF1 (TATA box binding protein (TBP)-associated factor, with molecular weight 250 kD, also known as TAFII250) is involved in the initiation of transcription by RNA polymerase II. It has histone acetyltransferase activity, which can relieve the binding between DNA and histones in the nucleosome. It is the largest subunit of the basal transcription factor, TFIID.
RNA polymerase II (N-20), N-terminus	GSE6390 (HeLa S3 cells) and GSE6392 (GM06990 cells)	RNA polymerase II (pol II) catalyzes transcription of DNA for the production of mRNAs and most snoRNAs.
RNA polymerase II (8WG16), C-terminus	GSE6391 (HeLa S3 cells) and GSE6394 (GM06990 cells)	RNA polymerase II (pol II) catalyzes transcription of DNA for the production of mRNAs and most snoRNAs. This antibody targets the pre-initiation complex form recognizing the C-terminal hexapeptide repeat of the large subunit of pol II. The initiation-complex form of RNA polymerase II is associated with the transcription start site.
H4Kac4	GSE6389 (HeLa S3 cells) and GSE6393 (GM06990 cells)	H4Kac4 (Histone H4 tetra-acetylated lysine) is a post-translational modification of the histone which affects chromatin remodeling. Histone H4 is found in transcriptionally active euchromatin.
H3K27me3	GSE8073 (HeLa S3 cells)	H3K27me3 (Histone H3 tri-methylated lysine) is a post-translational modification of the histone which affects chromatin remodeling. It is known to be associated with heterochromatin.
STAT1 p91 (C-24)	GSE6892 (HeLa S3 cells, interferon-alpha stimulated)	STAT1 (Signal Transducer and Activator of Transcription 1) responds to many cytokines and growth factors and regulates genes important for apoptosis, inflammation, and the immune system.
NFKB p65, N-terminus	GSE6900 (HeLa S3 cells, TNF-alpha stimulated)	NFKB p65 (RelA) is the strongest transcriptional-activator among the five members of the mammalian NF-kB/Rel family and plays an essential role in regulating the induction of genes involved in several physiological processes, including immune and inflammatory responses.
NFKB p65 (C-20), C-terminus	GSE6899 (HeLa S3 cells, TNF-alpha stimulated)	NFKB p65 (RelA) is the strongest transcriptional-activator among the five members of the mammalian NF-kB/Rel family and plays an essential role in regulating the induction of genes involved in several physiological processes, including immune and inflammatory responses.
SMARCA4/BRG1	GSE7370 (HeLa S3 cells)	SMARCA4 (BRG1) is a catalytic subunit of the SWI/SNF chromatin remodeling complex. It is a member of the SNF2 family of chromatin remodeling ATPases.
SMARCA6	GSE7371 (HeLa S3 cells)	SMARCA6 is a SNF2-like helicase linked to cell proliferation and DNA methylation. It is a member of the SNF2 family of chromatin remodeling ATPases.
NRSF	GSE7372 (HeLa S3 cells)	NRSF (neuron-restrictive silencer factor) represses neuron-specific genes in non-neuronal cells.

Display Conventions and Configuration

The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. Data may be thresholded by score and/or the user can specify the display of only the top N scoring items (default is 200) for all the subtracks. The score for each item is indicated in grayscale, with darker shades corresponding to higher scores. The details page for an item (displayed after clicking on an item in the track) shows the top 20 highest scoring items displayed in the current window.

Methods

The data from replicates were quantile-normalized and median-scaled to each other (both Cy3 and Cy5 channels). Using a 1000 bp sliding window centered on each oligonucleotide probe, a signal map (estimating the fold enrichment [log2 scale] of ChIP DNA) was generated by computing the pseudomedian signal of all log2(Cy5/Cy3) ratios (median of pairwise averages) within the window, including replicates. Using the same procedure, a -log10(P-value) map (measuring significance of enrichment of oligonucleotide probes in the window) for all sliding windows was made by computing P-values using the Wilcoxon paired signed rank test comparing fluorensent intensity between Cy5 and Cy3 for each oligonucleotide probe (Cy5 and Cy3 signals from the same array). A binding site was determined by thresholding oligonucleotide positions with -log10(P-value) (>= 4), extending qualified positions upstream and downstream 250 bp, and requiring 1000 bp space between two sites. Top 400 sites are retained for experiments (ENCODE Oct 2005 Freeze) and for the other datasets, sites found using 1, 5 and 10% false discovery rates (FDR) are displayed.

Verification

ChIP-chip binding sites were verified by comparing "hit lists" generated from combinations of different biological replicates. Only experiments that yielded a significant overlap (greater than 50 percent) were accepted. As an independent check (for maskless arrays), data on the microarray were randomized with respect to position and re-scored; significantly fewer hits (consistent with random noise) were generated this way. Sites for data from Nov. 2006, Jan. 2007, Apr. 2007 and Jun. 2007 were determined with false discovery rates (FDR) of 1%, 5% and 10%. The lowest FDR which includes each "Site" is displayed on that site's details page. For the ENCODE Oct 2005 Freeze data (BAF155, BAF170, Fos, Jun and TAF1 in HeLa S3 cells), the top 400 sites are shown.

Credits

These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University.

References

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004 Feb 20;116(4):499-509.

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.

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.

Quackenbush J. Microarray data normalization and transformation Nat Genet. 2002 Dec;32(Suppl):496-501.