diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.
diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.
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DOI：
10.1371/journal.pone.0065598
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Nestler EJ
中科院分区：
文献类型：
--
作者：
Shen L;Shao NY;Liu X;Maze I;Feng J;Nestler EJ
ChIP-SEQ越来越多地用于组蛋白修饰标记的全基因组图谱分析。尤其重要的是，比较两种不同情况下的芯片序列数据，例如疾病和对照，并识别在芯片浓缩方面显示差异的区域。我们已经开发了一个功能强大且易于使用的程序，名为DiffRep，可以从芯片序列数据中检测这些差异位点，无论是否有生物复制。此外，我们还开发了两个有用的工具，用于DiffRep程序包中的芯片序列分析：一个用于差异位点的注释，另一个用于寻找染色质修饰的“热点”。DiffRep是用Perl编程语言开发的，并作为命令行脚本在所有平台上运行。我们在两个不同的数据集上测试了DiffRep。一个是来自ENCODE项目的两个人类细胞系之间的H3K4me3的比较。另一项是比较可卡因和生理盐水处理条件下小鼠大脑中H3K9me3的离散区域。结果表明，在从CHIP-SEQ数据中检测差异位点方面，DiffRep是一种高度敏感的程序。
ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs. control, and identify regions that show differences in ChIP enrichment. We have developed a powerful and easy to use program, called diffReps, to detect those differential sites from ChIP-seq data, with or without biological replicates. In addition, we have developed two useful tools for ChIP-seq analysis in the diffReps package: one for the annotation of the differential sites and the other for finding chromatin modification “hotspots”. diffReps is developed in PERL programming language and runs on all platforms as a command line script. We tested diffReps on two different datasets. One is the comparison of H3K4me3 between two human cell lines from the ENCODE project. The other is the comparison of H3K9me3 in a discrete region of mouse brain between cocaine- and saline-treated conditions. The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
9.8
作者：
ENCODE Project Consortium
通讯作者：
ENCODE Project Consortium
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
30.5
作者：
Kidder, Benjamin L.;Hu, Gangqing;Zhao, Keji
通讯作者：
Zhao, Keji
影响因子：
64.5
作者：
Luco RF;Allo M;Schor IE;Kornblihtt AR;Misteli T
通讯作者：
Misteli T