Bono Hidemasa
Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.
Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan.
Antioxidants (Basel). 2021 Feb 25;10(3):345. doi: 10.3390/antiox10030345.
Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.
公共数据库中的数据积累导致了荟萃分析的广泛应用，荟萃分析是一种综合多项研究结果的统计分析方法。当自由基活性与抗氧化活性之间出现失衡时，就会发生氧化应激，这可以通过转录组分析在昆虫中进行研究。本研究旨在应用荟萃分析方法，利用公开可用的数据评估昆虫氧化转录组。我们通过人工筛选，主要从公共基因表达数据库中收集了多种昆虫物种的氧化应激反应相关RNA测序（RNA-seq）数据。仅发现了[具体物种]的RNA-seq数据，并使用新开发的针对无参考基因组序列物种的RNA-seq分析工作流程进行了系统分析。通过两种度量方法对结果进行评估，以构建氧化应激反应研究的参考数据集。通过基因富集分析发现，许多基因在氧化应激下被下调，并且与器官系统过程（GO:0003008）和黏着连接组织（GO:0034332）有关。还进行了跨物种分析。由于目前公共数据库中没有昆虫物种的RNA-seq数据，因此对[具体物种]的RNA-seq数据进行了筛选。这种方法，包括所开发的工作流程，是破译氧化应激反应中保守网络的有力工具。
