RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data.
RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data.
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DOI：
10.1186/s12864-018-5166-z
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发表时间：
2018-11-08
期刊：
影响因子：
4.4
通讯作者：
Ruggles KV
中科院分区：
文献类型：
--
作者：
Ernlund AW;Schneider RJ;Ruggles KV
翻译原子学数据，特别是全基因组核糖体分析和多核糖体分析，提供了多个水平的基因调控信息，可用于评估一般转录和翻译，以及翻译效率。这些技术的日益普及导致了多种检测翻译调控的算法，通常以命令行工具的形式分布，需要基本的编程能力。此外，由于当前软件的静态性质，不能充分实现动态转录和翻译比较分析。为了简化假设生成，调查人员必须能够实时操作和交互数据。为了解决当前软件缺乏集成的问题，我们引入了RIVET，核糖体研究和可视化来评估翻译，这是一个基于R shiny的图形用户界面，用于翻译组学数据探索和差异分析。RIVET可以分析来自多核糖体分析和核糖体分析实验的微阵列或RNA测序数据。RIVET为统计分析提供了多种选择，并集成了转录，翻译和翻译效率数据分析以及动态可视化所有结果的能力。RIVET是一个用户友好的工具，专为几乎没有编程背景的实验室科学家设计。RIVET促进了翻译组学数据的数据分析，允许基于用户定义的输入和出版准备可视化动态生成结果。我们希望RIVET将允许科学家有效地进行更全面的数据观察，这将导致关于翻译调控的更强大的假设。本文的在线版本（10.1186/s12864-018-5166-z）包含补充材料，可供授权用户使用。
Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, as well translational efficiency. The increasing popularity of these techniques has resulted in multiple algorithms to detect translational regulation, typically distributed in the form of command line tools that require a basic level of programming ability. Additionally, due to the static nature of current software, dynamic transcriptional and translational comparative analysis cannot be adequately achieved. In order to streamline hypothesis generation, investigators must have the ability to manipulate and interact with their data in real-time. To address the lack of integration in current software, we introduce RIVET, Ribosomal Investigation and Visualization to Evaluate Translation, an R shiny based graphical user interface for translatomics data exploration and differential analysis. RIVET can analyze either microarray or RNA sequencing data from polysome profiling and ribosome profiling experiments. RIVET provides multiple choices for statistical analysis as well as integration of transcription, translation, and translational efficiency data analytics and the ability to visualize all results dynamically. RIVET is a user-friendly tool designed for bench scientists with little to no programming background. RIVET facilitates the data analysis of translatomics data allowing for dynamic generation of results based on user-defined inputs and publication ready visualization. We expect RIVET will allow for scientists to efficiently make more comprehensive data observations that will lead to more robust hypothesis regarding translational regulation. The online version of this article (10.1186/s12864-018-5166-z) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK
影响因子：
7
作者：
Cenik C;Cenik ES;Byeon GW;Grubert F;Candille SI;Spacek D;Alsallakh B;Tilgner H;Araya CL;Tang H;Ricci E;Snyder MP
通讯作者：
Snyder MP
影响因子：
64.8
作者：
Hsieh, Andrew C.;Liu, Yi;Edlind, Merritt P.;Ingolia, Nicholas T.;Janes, Matthew R.;Sher, Annie;Shi, Evan Y.;Stumpf, Craig R.;Christensen, Carly;Bonham, Michael J.;Wang, Shunyou;Ren, Pingda;Martin, Michael;Jessen, Katti;Feldman, Morris E.;Weissman, Jonathan S.;Shokat, Kevan M.;Rommel, Christian;Ruggero, Davide
通讯作者：
Ruggero, Davide
影响因子：
5.8
作者：
Li, Wenzheng;Wang, Weili;Smith, Andrew D.
通讯作者：
Smith, Andrew D.