Dimont Emmanuel, Hofmann Oliver, Ho Sui Shannan J, Forrest Alistair R R, Kawaji Hideya, Hide Winston
Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA, RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan and RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.
Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA, RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan and RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA, RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan and RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.
Bioinformatics. 2014 Apr 15;30(8):1183-1184. doi: 10.1093/bioinformatics/btu125. Epub 2014 Mar 27.
Alternate promoter usage is an important molecular mechanism for generating RNA and protein diversity. Cap Analysis Gene Expression (CAGE) is a powerful approach for revealing the multiplicity of transcription start site (TSS) events across experiments and conditions. An understanding of the dynamics of TSS choice across these conditions requires both sensitive quantification and comparative visualization. We have developed CAGExploreR, an R package to detect and visualize changes in the use of specific TSS in wider promoter regions in the context of changes in overall gene expression when comparing different CAGE samples. These changes provide insight into the modification of transcript isoform generation and regulatory network alterations associated with cell types and conditions. CAGExploreR is based on the FANTOM5 and MPromDb promoter set definitions but can also work with user-supplied regions. The package compares multiple CAGE libraries simultaneously. Supplementary Materials describe methods in detail, and a vignette demonstrates a workflow with a real data example.
The package is freely available under the MIT license from CRAN (http://cran.r-project.org/web/packages/CAGExploreR).
edimont@mail.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
交替启动子使用是产生RNA和蛋白质多样性的重要分子机制。帽分析基因表达（CAGE）是一种强大的方法，可揭示跨实验和条件的转录起始位点（TSS）事件的多样性。要了解这些条件下TSS选择的动态变化，既需要灵敏的定量分析，也需要进行比较可视化。我们开发了CAGExploreR，这是一个R包，用于在比较不同CAGE样本时，在整体基因表达变化的背景下，检测和可视化更广泛启动子区域中特定TSS使用情况的变化。这些变化有助于深入了解与细胞类型和条件相关的转录本异构体生成的修饰以及调控网络的改变。CAGExploreR基于FANTOM5和MPromDb启动子集定义，但也可用于用户提供的区域。该包可同时比较多个CAGE文库。补充材料详细描述了方法，并且一个示例演示了使用真实数据的工作流程。
该包可根据MIT许可从CRAN（http://cran.r-project.org/web/packages/CAGExploreR）免费获取。
edimont@mail.harvard.edu 补充信息：补充数据可在《生物信息学》在线获取。
