Yale ChIP Super-track Settings
 
Yale ChIP-chip Tracks   (All Pilot ENCODE Chromatin Immunoprecipitation tracks)

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 All
Yale STAT1 pVal  Yale ChIP-chip (STAT1 ab, HeLa cells) P-Value  Data version: ENCODE June 2005 Freeze
Yale STAT1 Sig  Yale ChIP-chip (STAT1 ab, HeLa cells) Signal  Data version: ENCODE June 2005 Freeze
Yale STAT1 Sites  Yale ChIP-chip (STAT1 ab, HeLa cells) Binding Sites  Data version: ENCODE June 2005 Freeze
Yale ChIP pVal  Yale ChIP-chip P-Value  Data version: ENCODE Oct 2005 Freeze, Nov 2006, Jan 2007
Yale ChIP Signal  Yale ChIP-chip Signal  Data version: ENCODE Oct 2005 Freeze, Nov 2006, Jan 2007
Yale ChIP Sites  Yale ChIP-chip Sites  Data version: ENCODE Oct 2005 Freeze
Yale ChIP RFBR  Yale ChIP-chip Regulatory Factor Binding Regions Analysis  Data version: Dec 2005 Freeze

Overview

This super-track combines related tracks of ChIP-chip data generated by the Yale ENCODE group. ChIP-chip, also known as genome-wide location analysis, is a technique for isolation and identification of DNA sequences bound by specific proteins in cells, including histones. Histone methylation and acetylation serves as a stable genomic imprint that regulates gene expression and other epigenetic phenomena. These histones are found in transcriptionally active domains called euchromatin.

These tracks contain ChIP-chip data of multiple transcription factors such as STAT1 and histones in multiple cell lines such as HelaS3 (cervix epithelial adenocarcinoma). Data are displayed as signals, p-values and site predictions, as well as Regulatory Factor Binding Regions (RFBR) predictions.

Credits

These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University. The PCR Amplicon arrays were manufactured by Bing Ren's lab at UCSD.

The RFBR data set was made available by the Transcriptional Regulation Group of the ENCODE Project Consortium. The RFBR cluster and desert tracks were generated by Zhengdong Zhang from Mark Gerstein's group at Yale University.

References

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

Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P et al. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May;24(9):3804-14.

Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Res. 2003 Jul 1;31(13):3477-82.

Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P 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.

Efron B. Large-Scale Simultaneous Hypothesis Testing: The Choice of a Null Hypothesis. J Am Stat Assoc. 2004;99(465):96-104.

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein M. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 2007 Jun;17(6):787-97.