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二代测序数据的生物信息学分析确定了与2型糖尿病相关的分子生物标志物。

Bioinformatics Analysis of Next Generation Sequencing Data Identifies Molecular Biomarkers Associated With Type 2 Diabetes Mellitus.

作者信息

Alur Varun, Raju Varshita, Vastrad Basavaraj, Vastrad Chanabasayya, Kavatagimath Satish, Kotturshetti Shivakumar

机构信息

Department of Endocrinology, J.J.M Medical College, Davanagere, Karnataka, India.

Department of Obstetrics and Gynecology, J.J.M Medical College, Davanagere, Karnataka, India.

出版信息

Clin Med Insights Endocrinol Diabetes. 2023 Feb 20;16:11795514231155635. doi: 10.1177/11795514231155635. eCollection 2023.

DOI:10.1177/11795514231155635
PMID:36844983
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9944228/
Abstract

BACKGROUND

Type 2 diabetes mellitus (T2DM) is the most common metabolic disorder. The aim of the present investigation was to identify gene signature specific to T2DM.

METHODS

The next generation sequencing (NGS) dataset GSE81608 was retrieved from the gene expression omnibus (GEO) database and analyzed to identify the differentially expressed genes (DEGs) between T2DM and normal controls. Then, Gene Ontology (GO) and pathway enrichment analysis, protein-protein interaction (PPI) network, modules, miRNA (micro RNA)-hub gene regulatory network construction and TF (transcription factor)-hub gene regulatory network construction, and topological analysis were performed. Receiver operating characteristic curve (ROC) analysis was also performed to verify the prognostic value of hub genes.

RESULTS

A total of 927 DEGs (461 were up regulated and 466 down regulated genes) were identified in T2DM. GO and REACTOME results showed that DEGs mainly enriched in protein metabolic process, establishment of localization, metabolism of proteins, and metabolism. The top centrality hub genes , and were screened out as the critical genes. ROC analysis provides prognostic value of hub genes.

CONCLUSION

The potential crucial genes, especially , and , might be linked with risk of T2DM. Our study provided novel insights of T2DM into genetics, molecular pathogenesis, and novel therapeutic targets.

摘要

背景

2型糖尿病（T2DM）是最常见的代谢紊乱疾病。本研究的目的是鉴定T2DM特有的基因特征。

方法

从基因表达综合数据库（GEO）中检索下一代测序（NGS）数据集GSE81608，并进行分析以鉴定T2DM与正常对照之间的差异表达基因（DEG）。然后，进行基因本体（GO）和通路富集分析、蛋白质-蛋白质相互作用（PPI）网络、模块、微小RNA（miRNA）-枢纽基因调控网络构建和转录因子（TF）-枢纽基因调控网络构建以及拓扑分析。还进行了受试者工作特征曲线（ROC）分析以验证枢纽基因的预后价值。

结果

在T2DM中总共鉴定出927个DEG（461个上调基因和466个下调基因）。GO和REACTOME结果表明，DEG主要富集于蛋白质代谢过程、定位的建立、蛋白质代谢和新陈代谢。筛选出中心性最高的枢纽基因 、 和 作为关键基因。ROC分析提供了枢纽基因的预后价值。

结论

潜在的关键基因，尤其是 、 和 ，可能与T2DM的风险相关。我们的研究为T2DM的遗传学、分子发病机制和新的治疗靶点提供了新的见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/0d1f1da5806e/10.1177_11795514231155635-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/0a78d71b6d63/10.1177_11795514231155635-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/ce76dda329f9/10.1177_11795514231155635-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/e67e509c974f/10.1177_11795514231155635-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/679fe8ee16ea/10.1177_11795514231155635-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/5e9a57f135ed/10.1177_11795514231155635-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/6781fd78132b/10.1177_11795514231155635-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/cb43fc6a180e/10.1177_11795514231155635-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/0d1f1da5806e/10.1177_11795514231155635-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/0a78d71b6d63/10.1177_11795514231155635-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/ce76dda329f9/10.1177_11795514231155635-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/e67e509c974f/10.1177_11795514231155635-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/679fe8ee16ea/10.1177_11795514231155635-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/5e9a57f135ed/10.1177_11795514231155635-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/6781fd78132b/10.1177_11795514231155635-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/cb43fc6a180e/10.1177_11795514231155635-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/086a/9944228/0d1f1da5806e/10.1177_11795514231155635-fig8.jpg

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