Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues.
Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues.
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DOI：
10.1016/j.gene.2015.11.003
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发表时间：
2016-01
期刊：
影响因子：
3.5
通讯作者：
Jingyao Zeng;Shoucheng Liu;Yuhui Zhao;Xinyu Tan;H. Aljohi;Wanfei Liu;Songnian Hu
中科院分区：
文献类型：
--
作者：
Jingyao Zeng;Shoucheng Liu;Yuhui Zhao;Xinyu Tan;H. Aljohi;Wanfei Liu;Songnian Hu
近年来，RNA-seq因其单碱基准确性和高通量特性而成为广泛应用的转录组分析技术。在这项研究中，我们对15个正常小鼠组织的整合RNA-seq数据集应用计算方法，最终在UCSC RefGene注释中分配了8408个house-keeping （HK）基因和2581个组织特异性（TS）基因。除了一些基本的基因组特征外，我们还通过聚类、DAVID和Ingenuity pathway分析进行了表达、功能和通路分析，揭示了HK基因（基本过程）和TS基因（组织对应过程）的生理联系（组织）和多种生物学作用。此外，我们还利用RT-PCR方法对18个HK候选基因进行了检测，最终鉴定出一组新的高度稳定的内控基因：Ywhae、ddb1、Eif4h等。综上所述，本研究为进一步的遗传和进化研究提供了新的HK基因和TS基因资源，有助于我们更好地了解小鼠的形态发生和生物多样性。
Recently, RNA-seq has become widely used technology for transcriptome profiling due to its single-base accuracy and high-throughput speciality. In this study, we applied a computational approach on an integrated RNA-seq dataset across 15 normal mouse tissues, and consequently assigned 8408 house-keeping (HK) genes and 2581 tissue-specific (TS) genes among UCSC RefGene annotation. Apart from some basic genomic features, we also performed expression, function and pathway analysis with clustering, DAVID and Ingenuity Pathway Analysis, indicating the physiological connections (tissues) and diverse biological roles of HK genes (fundamental processes) and TS genes (tissue-corresponding processes). Moreover, we used RT-PCR method to test 18 candidate HK genes and finally identified a novel list of highly stable internal control genes:Ywhae,Ddb 1,Eif4h, etc. In summary, this study provides a new HK gene and TS gene resource for further genetic and evolution research and helps us better understand morphogenesis and biological diversity in mouse.