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Cistrome: an integrative platform for transcriptional regulation studies.

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/.

SUBMITTER: Liu T

PROVIDER: S-EPMC3245621 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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Cistrome: an integrative platform for transcriptional regulation studies.

Liu Tao T Ortiz Jorge A JA Taing Len L Meyer Clifford A CA Lee Bernett B Zhang Yong Y Shin Hyunjin H Wong Swee S SS Ma Jian J Lei Ying Y Pape Utz J UJ Poidinger Michael M Chen Yiwen Y Yeung Kevin K Brown Myles M Turpaz Yaron Y Liu X Shirley XS

Genome biology 20110822 8

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 e ...[more]

PMID: 21859476

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