Cistrome: an integrative platform for transcriptional regulation studies

被引：434

作者：

Liu, Tao ^{[1
,2
,3
]}

Ortiz, Jorge A. ^{[4
,5
]}

Taing, Len ^{[1
,2
,3
]}

Meyer, Clifford A. ^{[2
,3
]}

Lee, Bernett ^{[4
,6
]}

Zhang, Yong ^{[7
]}

Shin, Hyunjin ^{[1
,2
,3
]}

Wong, Swee S. ^{[4
,8
]}

Ma, Jian ^{[7
]}

Lei, Ying ^{[9
]}

Pape, Utz J. ^{[2
,3
]}

Poidinger, Michael ^{[4
,6
]}

Chen, Yiwen ^{[2
,3
]}

Yeung, Kevin ^{[4
,10
]}

Brown, Myles ^{[1
,11
,12
]}

Turpaz, Yaron ^{[4
,13
]}

Liu, X. Shirley ^{[1
,2
,3
]}

机构：

[1] Dana Farber Canc Inst, Ctr Funct Canc Epigenet, Boston, MA 02215 USA

[2] Harvard Univ, Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02215 USA

[3] Harvard Univ, Sch Publ Hlth, Boston, MA 02215 USA

[4] Lilly Singapore Ctr Drug Discovery, Singapore 138648, Singapore

[5] Beijing Genom Inst, Shenzhen 518083, Peoples R China

[6] Singapore Immunol Network, Singapore 138648, Singapore

[7] Tongji Univ, Sch Life Sci & Technol, Shanghai 200092, Peoples R China

[8] Eli Lilly & Co, Lilly Corp Ctr, Indianapolis, IN 46285 USA

[9] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA

[10] Jardine Lloyd Thompson Asia, Singapore 048583, Singapore

[11] Harvard Univ, Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA

[12] Harvard Univ, Sch Med, Boston, MA 02215 USA

[13] AstraZeneca Pharmaceut LP, Waltham, MA 02451 USA

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 08期

关键词：

DIFFERENTIAL EXPRESSION ANALYSIS; MODEL-BASED ANALYSIS; CHIP-CHIP; BINDING; BIOCONDUCTOR; ARCHIVE; ARRAYS; SITES;

D O I：

10.1186/gb-2011-12-8-r83

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/.

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