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Cistrome: an integrative platform for transcriptional regulation studies

Tao Liu12, Jorge A Ortiz34, Len Taing12, Clifford A Meyer1, Bernett Lee35, Yong Zhang6, Hyunjin Shin12, Swee S Wong37, Jian Ma6, Ying Lei8, Utz J Pape1, Michael Poidinger35, Yiwen Chen1, Kevin Yeung39, Myles Brown102*, Yaron Turpaz113* and X Shirley Liu12*

Author Affiliations

1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Ave, Boston, MA 02215, USA

2 Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA

3 Lilly Singapore Centre for Drug Discovery, 8A Biomedical Grove, Immunos, Singapore 138648

4 Beijing Genomics Institute, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China

5 Singapore Immunology Network, 8A Biomedical Grove, Immunos Building level 3, Singapore 138648

6 School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai 200092, China

7 Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA

8 Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA

9 Jardine Lloyd Thompson Asia, 1 Raffles Quay #27-01, One Raffles Quay - North Tower, Singapore 048583

10 Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave, Boston, MA 02215, USA

11 AstraZeneca Pharmaceuticals LP, 35 Gatehouse Drive, Waltham, MA 02451, USA

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Genome Biology 2011, 12:R83  doi:10.1186/gb-2011-12-8-r83

Published: 22 August 2011

Abstract

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/ webcite.