ChIP-Seq

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	ChIP-Seq Analysis Server
The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. This is an upgraded release that provides a richer collection of server-resident public data sets both from ChIP-seq experiments and the mass genome annotation data (MGA) of the Eukaryotic promoter database (EPD). Should you have any problem in using the new release, please switch to the old one. The programs offered by this web server are listed below.

ChIP-Seq Analysis Server

The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions.
This is an upgraded release that provides a richer collection of server-resident public data sets both from ChIP-seq experiments and the mass genome annotation data (MGA) of the Eukaryotic promoter database (EPD).
Should you have any problem in using the new release, please switch to the old one.
The programs offered by this web server are listed below.

Access to ChIP-Seq tools

ChIP-cor	Feature Correlation Tool
ChIP-center	Tag Centering Tool
ChIP-peak	Signal Peaks Detection Tool
ChIP-part	Partitioning Tool
ChIP-convert	Format Conversion Tool

WIG Files

WIG Files for public chIP-seq data

The source code is available on

Documentation
ChIP-Seq Tutorial ChIP-Seq Technical Document "Ambrosini et al. 2011, The ChIP-Seq server ..." (unpublished manuscript describing this web server) ChIP-Seq Project Contact Project Developers

Related Documentation on ChIP Experiments
PMID:17512414 High-resolution profiling of histone methylations in the human genome. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G,Chepelev I and Zhao K. Cell 2007, 129:823-837.
PMID:17392789 Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC and Pugh BF. Nature 2007, 446:572-576.
PMID:17603471 Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES and Bernstein BE. Nature 2007, 448:553-560.
PMID:17558387 Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M and Jones S. Nat Methods. 2007, Aug;4(8):613-4.
PMID:18243105 High-Resolution Mapping and Characterization of open chromatin across the genome. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS and Crawford GE. Cell 2008, 132:311-322.
PMID:18552846 Combinatorial patterns of histone acetylations and methylations in the human genome. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Nat Genet. 2008, Jul;40(7):897-903.
PMID:18329373 Dynamic regulation of nucleosome positioning in the human genome. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G and Zhao K. Cell. 2008 Mar 7;132(5):887-898.

Last update 13 Sep. 2010

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