## Description

This track shows the map of signal intensity (estimating the fold enrichment [log2 scale] of chromatin immunoprecipitated DNA vs. input DNA) 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

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## 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.

## 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.

## 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.