%0 Journal Article
%T Cistrome: an integrative platform for transcriptional regulation studies
%A Tao Liu
%A Jorge A Ortiz
%A Len Taing
%A Clifford A Meyer
%A Bernett Lee
%A Yong Zhang
%A Hyunjin Shin
%A Swee S Wong
%A Jian Ma
%A Ying Lei
%A Utz J Pape
%A Michael Poidinger
%A Yiwen Chen
%A Kevin Yeung
%A Myles Brown
%A Yaron Turpaz
%A X Shirley Liu
%J Genome Biology
%D 2011
%I BioMed Central
%R 10.1186/gb-2011-12-8-r83
%X The term 'cistrome' refers to the set of cis-acting targets of a trans-acting factor on a genome-wide scale, also known as the in vivo genome-wide location of transcription factors or histone modifications. Cistromes were initially identified using chromatin immunoprecipitation (ChIP) combined with microarrays (ChIP-chip) [1]. However, with the recent advent of next generation sequencing (NGS) technologies, ChIP combined with NGS (ChIP-seq) [2] has become the more popular technique due to its higher sensitivity and resolution.Computational analyses of cistrome data have become increasingly complex and integrative. Investigators often examine the data from many different angles by combining cistrome, epigenome, genomic sequence, and transcriptome analyses. Many algorithms and tools have been published over the years to facilitate such analyses. However, these tools require investigators to have both the hardware resources and computational expertise to install, configure, and run these different algorithms effectively. Integrated platforms such as CisGenome [3] and seqMINER [4] have been developed to streamline data analyses; however, the maintenance of these platforms demands suitable hardware resources and computational skills. In addition, these tools lack useful features such as the integration of cistrome data with gene expression analysis, data sharing between researchers, and reusable analysis workflows.To address the above challenges, we developed the Cistrome platform to provide a flexible bioinformatics workbench with an analysis platform for ChIP-chip/seq and gene expression microarray analysis. Cistrome was built on top of Galaxy [5], an open-source web based computational framework that allows the easy integration of different tools. Cistrome integrates useful functions specific for ChIP-chip/seq and gene expression analyses. These functions were implemented in a modular fashion to allow easy incorporation of new tools in the future. Cistrome was deploye
%U http://genomebiology.com/2011/12/8/R83