Suzuki Takayuki, Ono Yoko, 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.
Biomedicines. 2021 Dec 3;9(12):1830. doi: 10.3390/biomedicines9121830.
Analysis of RNA-sequencing (RNA-seq) data is an effective means to analyze the gene expression levels under specific conditions and discover new biological knowledge. More than 74,000 experimental series with RNA-seq have been stored in public databases as of 20 October 2021. Since this huge amount of expression data accumulated from past studies is a promising source of new biological insights, we focused on a meta-analysis of 1783 runs of RNA-seq data under the conditions of two types of stressors: oxidative stress (OS) and hypoxia. The collected RNA-seq data of OS were organized as the OS dataset to retrieve and analyze differentially expressed genes (DEGs). The OS-induced DEGs were compared with the hypoxia-induced DEGs retrieved from a previous study. The results from the meta-analysis of OS transcriptomes revealed two genes, and , which were particularly downregulated, suggesting a relationship between OS and zinc homeostasis. The comparison between meta-analysis of OS and hypoxia showed that several genes were differentially expressed under both stress conditions, and it was inferred that the downregulation of cell cycle-related genes is a mutual biological process in both OS and hypoxia.
RNA测序（RNA-seq）数据分析是分析特定条件下基因表达水平并发现新生物学知识的有效手段。截至2021年10月20日，超过74000个RNA-seq实验系列已存储在公共数据库中。由于过去研究积累的大量表达数据是新生物学见解的一个有前景的来源，我们专注于对1783次RNA-seq数据在两种应激源条件下进行荟萃分析：氧化应激（OS）和缺氧。将收集到的OS的RNA-seq数据整理为OS数据集，以检索和分析差异表达基因（DEG）。将OS诱导的DEG与先前研究中检索到的缺氧诱导的DEG进行比较。OS转录组的荟萃分析结果揭示了两个基因， 和 ，它们特别下调，表明OS与锌稳态之间存在关系。OS和缺氧的荟萃分析比较表明，几个基因在两种应激条件下均差异表达，并且推断细胞周期相关基因的下调是OS和缺氧中的共同生物学过程。
