CoCAS: a ChIP-on-chip analysis suite

被引：17

作者：

Benoukraf, Touati ^{[1
,2
,3
,4
]}

Cauchy, Pierre ^{[4
,5
]}

Fenouil, Romain ^{[1
,2
,3
,4
]}

Jeanniard, Adrien ^{[1
,2
,3
,4
]}

Koch, Frederic ^{[1
,2
,3
,4
]}

Jaeger, Sebastien ^{[1
,2
,3
,4
]}

Thieffry, Denis ^{[4
,5
]}

Imbert, Jean ^{[4
,5
]}

Andrau, Jean-Christophe ^{[1
,2
,3
,4
]}

Spicuglia, Salvatore ^{[1
,2
,3
,4
]}

Ferrier, Pierre ^{[1
,2
,3
,4
]}

机构：

[1] Ctr Immunol Marseille Luminy, Marseille, France

[2] UMR6102, CNRS, Marseille, France

[3] U631, INSERM, Marseille, France

[4] Univ Mediterranee, Marseille, France

[5] TAGC, U928, INSERM, Marseille, France

来源：

BIOINFORMATICS | 2009年 / 25卷 / 07期

关键词：

NORMALIZATION; MODEL;

D O I：

10.1093/bioinformatics/btp075

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by this approach, we have developed ChIP-on-chip Analysis Suite (CoCAS), a standalone software suite which implements optimized ChIP-on-chip data normalization, improved peak detection, as well as quality control reports. Our software allows dye swap, replicate correlation and connects easily with genome browsers and other peak detection algorithms. CoCAS can readily be used on the latest generation of Agilent high-density arrays. Also, the implemented peak detection methods are suitable for other datasets, including ChIP-Seq output.

引用

页码：954 / 955

页数：2

共 10 条

[1] Computational epigenetics [J].

Bock, Christoph ;

Lengauer, Thomas .

BIOINFORMATICS, 2008, 24 (01) :1-10

[2] Polycomb complexes repress developmental regulators in murine embryonic stem cells [J].

Boyer, LA ;

Plath, K ;

Zeitlinger, J ;

Brambrink, T ;

Medeiros, LA ;

Lee, TI ;

Levine, SS ;

Wernig, M ;

Tajonar, A ;

Ray, MK ;

Bell, GW ;

Otte, AP ;

Vidal, M ;

Gifford, DK ;

Young, RA ;

Jaenisch, R .

NATURE, 2006, 441 (7091) :349-353

[3]

Huber Wolfgang, 2002, Bioinformatics, V18 Suppl 1, pS96

[4] Normalization and experimental design for ChIP-chip data [J].

Peng, Shouyong ;

Alekseyenko, Artyom A. ;

Larschan, Erica ;

Kuroda, Mitzi I. ;

Park, Peter J. .

BMC BIOINFORMATICS, 2007, 8 (1)

[5] Genome-wide location and function of DNA binding proteins [J].

Ren, B ;

Robert, F ;

Wyrick, JJ ;

Aparicio, O ;

Jennings, EG ;

Simon, I ;

Zeitlinger, J ;

Schreiber, J ;

Hannett, N ;

Kanin, E ;

Volkert, TL ;

Wilson, CJ ;

Bell, SP ;

Young, RA .

SCIENCE, 2000, 290 (5500) :2306-+

[6]

Smyth G. K., 2004, Stat. Appl. Genet. Mol. Biol, V3, pArticl, DOI [10.2202/1544-6115.1027, DOI 10.2202/1544-6115.1027]

[7] Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts [J].

Toedling, Joern ;

Sklyar, Oleg ;

Huber, Wolfgang .

BMC BIOINFORMATICS, 2007, 8 (1)

[8] Rosetta error model for gene expression analysis [J].

Weng, L ;

Dai, HY ;

Zhan, YH ;

He, YD ;

Stepaniants, SB ;

Bassett, DE .

BIOINFORMATICS, 2006, 22 (09) :1111-1121

[9] Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation [J].

Yang, YH ;

Dudoit, S ;

Luu, P ;

Lin, DM ;

Peng, V ;

Ngai, J ;

Speed, TP .

NUCLEIC ACIDS RESEARCH, 2002, 30 (04) :e15

[10] ChIP-chip: Data, model, and analysis [J].

Zheng, Ming ;

Barrera, Leah O. ;

Ren, Bing ;

Wu, Ying Nian .

BIOMETRICS, 2007, 63 (03) :787-796

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