ChIP-Seq

ChIP-Seq Analysis Server

The ChIP-Seq Server aims at providing tools for the analysis of ChIP-seq data and other types of MGA (mass genome annotation data).
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
WIG Files WIG Files for public chIP-seq data

The source code is available on

Documentation
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 Feb. 2010