Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan.
Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
Life Sci Alliance. 2022 Oct 10;6(1). doi: 10.26508/lsa.202201518. Print 2023 Jan.
Gene expression studies are intrinsically biased, with many studies influenced by concomitant information such as gene-disease associations. This limitation can be overcome using a data-driven analysis approach without relying on ancillary information. The FANTOM CAGE-Associated Transcriptome project provides a comprehensive meta-assembly of the human transcriptome using coding and noncoding genes. Hypoxia strongly influences gene expression; in addition, noncoding RNA (ncRNA) metabolism is down-regulated in response to hypoxic stimuli. We evaluated the differential response of various transcripts to hypoxia by determining their hypoxia responsiveness scores. Enrichment analysis revealed that several genes associated with ncRNA metabolism, particularly those involved in ribosomal RNA processing, were down-regulated in response to hypoxia. Previously published information from the FANTOM CAGE-Associated Transcriptome project was suitable for meta-analysis of the transcriptome sequencing data from both coding and ncRNAs and to evaluate the hypoxia responsiveness of target transcripts and relationship between sense-antisense transcripts from the same locus. Our results may facilitate functional annotation of various transcripts including ncRNAs, allowing for both sense and antisense and coding and noncoding evaluations.
基因表达研究本质上存在偏差，许多研究受到伴随信息的影响，如基因-疾病关联。这种局限性可以通过不依赖辅助信息的数据驱动分析方法来克服。FANTOM CAGE 相关转录组项目使用编码和非编码基因提供了人类转录组的综合元组装。缺氧强烈影响基因表达；此外，非编码 RNA（ncRNA）代谢会因缺氧刺激而下调。我们通过确定它们的缺氧反应分数来评估各种转录物对缺氧的差异反应。富集分析表明，与 ncRNA 代谢相关的几个基因，特别是涉及核糖体 RNA 加工的基因，在缺氧反应中下调。先前从 FANTOM CAGE 相关转录组项目中发布的信息适用于来自编码和 ncRNA 的转录组测序数据的荟萃分析，以及评估靶转录物的缺氧反应性以及来自同一基因座的有义-反义转录物之间的关系。我们的结果可能有助于包括 ncRNA 在内的各种转录物的功能注释，允许进行有义、反义、编码和非编码评估。
