将总 RNA 作为发育神经毒性的潜在生物标志物进行硅学分析。

IF 2.2 3区 医学 Q2 HEALTH CARE SCIENCES & SERVICES
Snežana M Jovičić
{"title":"将总 RNA 作为发育神经毒性的潜在生物标志物进行硅学分析。","authors":"Snežana M Jovičić","doi":"10.1177/14604582241285832","DOIUrl":null,"url":null,"abstract":"<p><p>A vast number of neurodegenerative disorders arise from neurotoxicity. In neurotoxicity, more than 250 RNA molecules are up and downregulated. The manuscript investigates the exposure of chlorpyrifos organophosphate pesticide (COP) effect on total RNA in murine brain tissue in 4 genotypes for in silico neurodegeneration development. The GSE58103 dataset from the Gene Expression Omnibus (GEO) database applies for data preprocessing, normalization, and quality control. Differential expression analysis (DEG) uses the limma package in R. Study compared expression profiles from murine fetal brain tissues across four genotypes: PON-1 knockout (KO), tgHuPON1Q192 (Q-tg), tgHuPON1R192 (R-tg), and wild-type (WT). We analyze 60 samples, 15 samples per genotype, to identify DEGs. The significance criteria are adjusted <i>p</i>-value <.05 and a |log2 fold change| > 1. The study identifies microRNA485 as the potential biomarker of COP toxicity using the GSE58103 dataset. Significant differences exist for microRNA485 between KO and WT groups by differential expression analysis. Moreover, graphical analysis shows sample relationships among genotype groups. MicroRNA485 represents a promising biomarker for developmental COP neurotoxicity by utilizing in silico analysis in scientific practice.</p>","PeriodicalId":55069,"journal":{"name":"Health Informatics Journal","volume":"30 4","pages":"14604582241285832"},"PeriodicalIF":2.2000,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Analysis of total RNA as a potential biomarker of developmental neurotoxicity in silico.\",\"authors\":\"Snežana M Jovičić\",\"doi\":\"10.1177/14604582241285832\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>A vast number of neurodegenerative disorders arise from neurotoxicity. In neurotoxicity, more than 250 RNA molecules are up and downregulated. The manuscript investigates the exposure of chlorpyrifos organophosphate pesticide (COP) effect on total RNA in murine brain tissue in 4 genotypes for in silico neurodegeneration development. The GSE58103 dataset from the Gene Expression Omnibus (GEO) database applies for data preprocessing, normalization, and quality control. Differential expression analysis (DEG) uses the limma package in R. Study compared expression profiles from murine fetal brain tissues across four genotypes: PON-1 knockout (KO), tgHuPON1Q192 (Q-tg), tgHuPON1R192 (R-tg), and wild-type (WT). We analyze 60 samples, 15 samples per genotype, to identify DEGs. The significance criteria are adjusted <i>p</i>-value <.05 and a |log2 fold change| > 1. The study identifies microRNA485 as the potential biomarker of COP toxicity using the GSE58103 dataset. Significant differences exist for microRNA485 between KO and WT groups by differential expression analysis. Moreover, graphical analysis shows sample relationships among genotype groups. MicroRNA485 represents a promising biomarker for developmental COP neurotoxicity by utilizing in silico analysis in scientific practice.</p>\",\"PeriodicalId\":55069,\"journal\":{\"name\":\"Health Informatics Journal\",\"volume\":\"30 4\",\"pages\":\"14604582241285832\"},\"PeriodicalIF\":2.2000,\"publicationDate\":\"2024-10-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Health Informatics Journal\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1177/14604582241285832\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"HEALTH CARE SCIENCES & SERVICES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Health Informatics Journal","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1177/14604582241285832","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"HEALTH CARE SCIENCES & SERVICES","Score":null,"Total":0}
引用次数: 0

摘要

大量神经退行性疾病都源于神经毒性。在神经毒性中,有超过 250 种 RNA 分子被上调或下调。本手稿研究了暴露于毒死蜱有机磷农药(COP)对4种基因型小鼠脑组织总RNA的影响,以进行神经退行性病变的硅学研究。基因表达总库(GEO)数据库中的 GSE58103 数据集用于数据预处理、归一化和质量控制。研究比较了四种基因型的小鼠胎儿脑组织表达谱:PON-1基因敲除(KO)、tgHuPON1Q192(Q-tg)、tgHuPON1R192(R-tg)和野生型(WT)。我们分析了 60 个样本,每个基因型 15 个样本,以确定 DEGs。显著性标准为调整后的 p 值 1。该研究利用 GSE58103 数据集确定 microRNA485 为 COP 毒性的潜在生物标记物。通过差异表达分析,microRNA485 在 KO 组和 WT 组之间存在显著差异。此外,图形分析显示了基因型组间的样本关系。通过在科学实践中利用硅分析,MicroRNA485有望成为COP神经毒性发育的生物标记物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Analysis of total RNA as a potential biomarker of developmental neurotoxicity in silico.

A vast number of neurodegenerative disorders arise from neurotoxicity. In neurotoxicity, more than 250 RNA molecules are up and downregulated. The manuscript investigates the exposure of chlorpyrifos organophosphate pesticide (COP) effect on total RNA in murine brain tissue in 4 genotypes for in silico neurodegeneration development. The GSE58103 dataset from the Gene Expression Omnibus (GEO) database applies for data preprocessing, normalization, and quality control. Differential expression analysis (DEG) uses the limma package in R. Study compared expression profiles from murine fetal brain tissues across four genotypes: PON-1 knockout (KO), tgHuPON1Q192 (Q-tg), tgHuPON1R192 (R-tg), and wild-type (WT). We analyze 60 samples, 15 samples per genotype, to identify DEGs. The significance criteria are adjusted p-value <.05 and a |log2 fold change| > 1. The study identifies microRNA485 as the potential biomarker of COP toxicity using the GSE58103 dataset. Significant differences exist for microRNA485 between KO and WT groups by differential expression analysis. Moreover, graphical analysis shows sample relationships among genotype groups. MicroRNA485 represents a promising biomarker for developmental COP neurotoxicity by utilizing in silico analysis in scientific practice.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Health Informatics Journal
Health Informatics Journal HEALTH CARE SCIENCES & SERVICES-MEDICAL INFORMATICS
CiteScore
7.80
自引率
6.70%
发文量
80
审稿时长
6 months
期刊介绍: Health Informatics Journal is an international peer-reviewed journal. All papers submitted to Health Informatics Journal are subject to peer review by members of a carefully appointed editorial board. The journal operates a conventional single-blind reviewing policy in which the reviewer’s name is always concealed from the submitting author.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信