Protocol for comparing gene-level selection on coding mutations between two groups of samples with Coselens.
Protocol for comparing gene-level selection on coding mutations between two groups of samples with Coselens.
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DOI：
10.1016/j.xpro.2023.102117
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发表时间：
2023-03-17
期刊：
影响因子：
--
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Iranzo J;Gruenhagen G;Calle-Espinosa J;Koonin EV
对在条件选择下进化的基因的研究可以揭示适应的基因组基础，揭示上位性和表型可塑性。该方案描述了如何使用Coselens软件包比较两组样本之间的基因水平选择。安装Coselens并准备好数据集后，在笔记本电脑上运行一次典型的时间不到10分钟。Coselens最适合分析体细胞突变和实验进化的数据，因为独立进化的样本是可用的。有关本方案使用和执行的完整详细信息，请参见Irenzo et al.（2022年）。Coselens基于编码突变量化基因水平的条件选择在笔记本电脑上分析中等大小的数据集，不到10分钟从全基因组或靶向测序中输入突变表输出受条件选择影响的基因、效应量和p值出版商说明：进行任何实验方案都需要遵守当地机构的实验室安全和伦理指南。对在条件选择下进化的基因的研究可以揭示适应的基因组基础，揭示上位性和表型可塑性。该方案描述了如何使用Coselens软件包比较两组样本之间的基因水平选择。安装Coselens并准备好数据集后，在笔记本电脑上运行一次典型的时间不到10分钟。Coselens最适合分析体细胞突变和实验进化的数据，因为独立进化的样本是可用的。
The study of genes that evolve under conditional selection can shed light on the genomic underpinnings of adaptation, revealing epistasis and phenotypic plasticity. This protocol describes how to use the Coselens package to compare gene-level selection between two groups of samples. After installing Coselens and preparing the datasets, a typical run on a laptop takes less than 10 min. Coselens is best suited to analyze somatic mutations and data from experimental evolution, for which independently evolved samples are available. For complete details on the use and execution of this protocol, please refer to Iranzo et al. (2022). Coselens quantifies gene-level conditional selection based on coding mutations Analyze medium-size datasets on a laptop in less than 10 min Input mutation tables from whole-genome or targeted sequencing Output genes subject to conditional selection, effect sizes, and p values Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. The study of genes that evolve under conditional selection can shed light on the genomic underpinnings of adaptation, revealing epistasis and phenotypic plasticity. This protocol describes how to use the Coselens package to compare gene-level selection between two groups of samples. After installing Coselens and preparing the datasets, a typical run on a laptop takes less than 10 min. Coselens is best suited to analyze somatic mutations and data from experimental evolution, for which independently evolved samples are available.
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DOI：
10.1073/pnas.1807256115
发表时间：
2018-11-20
影响因子：
11.1
作者：
Persi E;Wolf YI;Leiserson MDM;Koonin EV;Ruppin E
通讯作者：
Ruppin E
影响因子：
64.5
作者：
Martincorena I;Raine KM;Gerstung M;Dawson KJ;Haase K;Van Loo P;Davies H;Stratton MR;Campbell PJ
通讯作者：
Campbell PJ
影响因子：
8.8
作者：
Iranzo, Jaime;Gruenhagen, George;V. Koonin, Eugene
通讯作者：
V. Koonin, Eugene
影响因子：
5.8
作者：
Zhao, Hao;Sun, Zhifu;Wang, Liguo
通讯作者：
Wang, Liguo
影响因子：
9.3
作者：
Ellrott K;Bailey MH;Saksena G;Covington KR;Kandoth C;Stewart C;Hess J;Ma S;Chiotti KE;McLellan M;Sofia HJ;Hutter C;Getz G;Wheeler D;Ding L;MC3 Working Group;Cancer Genome Atlas Research Network
通讯作者：
Cancer Genome Atlas Research Network