RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.
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DOI：
10.1093/bioinformatics/btw585
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发表时间：
2017-01-01
期刊：
影响因子：
--
通讯作者：
Rätsch G
中科院分区：
文献类型：
--
作者：
Zhong Y;Karaletsos T;Drewe P;Sreedharan VT;Kuo D;Singh K;Wendel HG;Rätsch G
基于深度测序的核糖体足迹分析可以为蛋白质翻译的调控机制提供新的见解。然而，观察到的核糖体谱从根本上被转录活性所混淆。为了破译翻译监管的原理，需要能够可靠地检测病例对照研究中翻译效率变化的工具。我们提出了一个统计框架和一个分析工具 RiboDiff，用于检测实验处理中翻译效率变化的基因。 RiboDiff 使用广义线性模型分别估计 RNA-Seq 和核糖体分析测量的过度分散，并使用 mRNA 丰度和核糖体占用率对差异翻译效率进行统计测试。 RiboDiff 网页 http://bioweb.me/ribodiff。包括用于预处理 FASTQ 数据的脚本的源代码可从 http://github.com/ratschlab/ribodiff 获取。 补充数据可在生物信息学在线获取。
Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case–control studies are needed. We present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy. RiboDiff webpage http://bioweb.me/ribodiff. Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff. Supplementary data are available at Bioinformatics online.
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影响因子：
30.5
作者：
Su X;Yu Y;Zhong Y;Giannopoulou EG;Hu X;Liu H;Cross JR;Rätsch G;Rice CM;Ivashkiv LB
通讯作者：
Ivashkiv LB
影响因子：
14.9
作者：
Drewe P;Stegle O;Hartmann L;Kahles A;Bohnert R;Wachter A;Borgwardt K;Rätsch G
通讯作者：
Rätsch G
影响因子：
14.8
作者：
Ingolia, Nicholas T.;Brar, Gloria A.;Rouskin, Silvia;McGeachy, Anna M.;Weissman, Jonathan S.
通讯作者：
Weissman, Jonathan S.
影响因子：
5.8
作者：
Olshen, Adam B.;Hsieh, Andrew C.;Taylor, Barry S.
通讯作者：
Taylor, Barry S.
影响因子：
64.8
作者：
Wolfe, Andrew L.;Singh, Kamini;Zhong, Yi;Drewe, Philipp;Rajasekhar, Vinagolu K.;Sanghvi, Viraj R.;Mavrakis, Konstantinos J.;Jiang, Man;Roderick, Justine E.;Van der Meulen, Joni;Schatz, Jonathan H.;Rodrigo, Christina M.;Zhao, Chunying;Rondou, Pieter;de Stanchina, Elisa;Teruya-Feldstein, Julie;Kelliher, Michelle A.;Speleman, Frank;Porco, John A., Jr.;Pelletier, Jerry;Raetsch, Gunnar;Wendel, Hans-Guido
通讯作者：
Wendel, Hans-Guido