PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
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DOI：
10.1186/1471-2105-11-415
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发表时间：
2010-08-06
影响因子：
3
通讯作者：
Bertone P
中科院分区：
文献类型：
--
作者：
Salmon-Divon M;Dvinge H;Tammoja K;Bertone P
功能基因组研究涉及高通量测序和平铺阵列应用（例如 ChIP-seq 和 ChIP-chip），在所研究的基因组中产生大量实验衍生的信号峰。在分析这些基因座以确定其潜在的调控功能时，必须考虑相对于近端基因和整个目标基因组中注释的调控元件的信号富集区域。转录调控因子的染色质关联区域应区分为单独的结合位点，以增强下游分析，例如识别已知和新颖的共有基序。 PeakAnalyzer 是一组高性能实用程序，用于自动处理实验衍生的峰区域和基因组位点注释。该程序可以准确地将信号富集的多模态区域细分为与结合位点或染色质修饰相对应的不同亚峰，检索包含计算出的亚峰峰的基因组序列，并识别感兴趣的位置特征，例如与外显子/内含子基因组件的交叉、邻近上下游转录起始位点和顺式调控元件。该软件可以配置为作为高通量分析的管道组件运行，也可以作为具有直观用户界面的跨平台桌面应用程序运行。 PeakAnalyzer 包含许多 ChIP-seq 和 ChIP 芯片数据分析所必需的实用程序。为 Unix 管道集成提供高性能实现以及用于交互式使用的 GUI 版本。提供了 C++ 和 Java 源代码，以及 Linux、Mac OS X 和 Windows 系统的本机二进制文件。
Functional genomic studies involving high-throughput sequencing and tiling array applications, such as ChIP-seq and ChIP-chip, generate large numbers of experimentally-derived signal peaks across the genome under study. In analyzing these loci to determine their potential regulatory functions, areas of signal enrichment must be considered relative to proximal genes and regulatory elements annotated throughout the target genome Regions of chromatin association by transcriptional regulators should be distinguished as individual binding sites in order to enhance downstream analyses, such as the identification of known and novel consensus motifs. PeakAnalyzer is a set of high-performance utilities for the automated processing of experimentally-derived peak regions and annotation of genomic loci. The programs can accurately subdivide multimodal regions of signal enrichment into distinct subpeaks corresponding to binding sites or chromatin modifications, retrieve genomic sequences encompassing the computed subpeak summits, and identify positional features of interest such as intersection with exon/intron gene components, proximity to up- or downstream transcriptional start sites and cis-regulatory elements. The software can be configured to run either as a pipeline component for high-throughput analyses, or as a cross-platform desktop application with an intuitive user interface. PeakAnalyzer comprises a number of utilities essential for ChIP-seq and ChIP-chip data analysis. High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. Source code in C++ and Java is provided, as are native binaries for Linux, Mac OS X and Windows systems.
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影响因子：
46.9
作者：
Ji, Hongkai;Jiang, Hui;Ma, Wenxiu;Johnson, David S.;Myers, Richard M.;Wong, Wing H.
通讯作者：
Wong, Wing H.
影响因子：
5.8
作者：
Alekseyenko, Alexander V.;Lee, Christopher J.
通讯作者：
Lee, Christopher J.
影响因子：
3
作者：
Nix DA;Courdy SJ;Boucher KM
通讯作者：
Boucher KM
DOI：
10.1126/science.1160930
发表时间：
2008-10-17
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Wilson MD;Barbosa-Morais NL;Schmidt D;Conboy CM;Vanes L;Tybulewicz VL;Fisher EM;Tavaré S;Odom DT
通讯作者：
Odom DT
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS