Annotation depth confounds direct comparison of gene expression across species.
Annotation depth confounds direct comparison of gene expression across species.
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DOI：
10.1186/s12859-021-04414-y
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发表时间：
2021-10-15
影响因子：
3
通讯作者：
Martin M
中科院分区：
文献类型：
--
作者：
Oziolor E;Arat S;Martin M
生物体之间分子框架的比较可以在结构和功能水平上进行。最常见的自上而下的功能比较方法之一是 RNA 测序。这种对有机体转录反应的估计对于理解分子活性的进化很有意义，分子活性的进化可用于回答从基础生物学到临床前物种选择和翻译的各种问题。然而，物种之间的直接比较往往受到分子框架结构的进化差异以及人类和其他物种之间遗传背景理解深度的巨大差异的阻碍。在这里，我们重点关注后者。我们试图了解转录组注释的差异如何影响物种之间的直接基因丰度比较。考虑到当前可用的工具，并使用来自人类、食蟹猴、狗、大鼠和小鼠的样本数据集以及常见的定量和标准化方法，我们检查并提出了一些直接比较的简单方法。此外，我们还研究了跨物种基因组注释深度和质量的变化如何影响这些直接比较。我们的研究结果表明，进一步努力开发更好的基因组注释或计算标准化工具可能会引起人们的强烈兴趣。在线版本包含可在 10.1186/s12859-021-04414-y 获取的补充材料。
Comparisons of the molecular framework among organisms can be done on both structural and functional levels. One of the most common top-down approaches for functional comparisons is RNA sequencing. This estimation of organismal transcriptional responses is of interest for understanding evolution of molecular activity, which is used for answering a diversity of questions ranging from basic biology to pre-clinical species selection and translation. However, direct comparison between species is often hindered by evolutionary divergence in structure of molecular framework, as well as large difference in the depth of our understanding of the genetic background between humans and other species. Here, we focus on the latter. We attempt to understand how differences in transcriptome annotation affect direct gene abundance comparisons between species. We examine and suggest some straightforward approaches for direct comparison given the current available tools and using a sample dataset from human, cynomolgus monkey, dog, rat and mouse with a common quantitation and normalization approach. In addition, we examine how variation in genome annotation depth and quality across species may affect these direct comparisons. Our findings suggest that further efforts for better genome annotation or computational normalization tools may be of strong interest. The online version contains supplementary material available at 10.1186/s12859-021-04414-y.
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影响因子：
12.3
作者：
Robinson MD;Oshlack A
通讯作者：
Oshlack A
影响因子：
7
作者：
Chen, Jenny;Swofford, Ross;Regev, Aviv
通讯作者：
Regev, Aviv
影响因子：
3
作者：
Smid M;Coebergh van den Braak RRJ;van de Werken HJG;van Riet J;van Galen A;de Weerd V;van der Vlugt-Daane M;Bril SI;Lalmahomed ZS;Kloosterman WP;Wilting SM;Foekens JA;IJzermans JNM;MATCH study group;Martens JWM;Sieuwerts AM
通讯作者：
Sieuwerts AM
DOI：
10.1073/pnas.1413624111
发表时间：
2014-12-02
影响因子：
11.1
作者：
Lin, Shin;Lin, Yiing;Snyder, Michael P.
通讯作者：
Snyder, Michael P.
影响因子：
4.4
作者：
Zhang C;Zhang B;Lin LL;Zhao S
通讯作者：
Zhao S