tailieunhanh - Báo cáo y học: " Cistrome: an integrative platform for transcriptional regulation studies"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Cistrome: an integrative platform for transcriptional regulation studies. | Liu et al. Genome Biology 2011 12 R83 http 2011 12 8 R83 Genome Biology SOFTWARE Open Access Cistrome an integrative platform for transcriptional regulation studies Tao Liu1 2t Jorge A Ortiz3 4t Len Taing1 2 Clifford A Meyer1 2 Bernett Lee3 5 Yong Zhang6 Hyunjin Shin1 2 Q A OO Q lA oinn3 7 Ii n í lo6 Vin n I Cli8 I t 7 I Dof iCi1 Dr iiHinnor3 5 VnA cifi rhon1 ICowin Vol mn3 9 Swee S Wong Jian Ma ling Lei Utz J Pape Michael Poidingei livven Chen Kevin leung Myles Brown2 10 Yaron Turpaz3 11 and X Shirley Liu1 2 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 ChlP-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 ap . Rationale 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. Cis-tromes 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 .