Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing.

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY

Accounts of Chemical Research Pub Date : 2023-12-31 DOI:10.22074/cellj.2023.2007217.1368

Mansoureh Farhangniya, Farzaneh Mohamadi Farsani, Najmeh Salehi, Ali Samadikuchaksaraei

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引用次数: 0

Abstract

Objective: Wound healing is a complex process involving the coordinated interaction of various genes and molecular
pathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug development
to improve successful wound repair interventions.
Materials and Methods: This study is a network-meta analysis study. Nine wound healing microarray datasets obtained
from the Gene Expression Omnibus (GEO) database were used for this study. Differentially expressed genes (DEGs)
were described using the Limma package and shared genes were used as input for weighted gene co-expression
network analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of a
protein-protein interaction (PPI) network was achieved by the STRING and Cytoscape.
Results: A total of 424 DEGs were determined. A co-expression network was constructed using 7692 shared genes
between nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20
genes of up and down-regulation were selected. The top down-regulated genes, including TJP1, SEC61A1, PLEK,
ATP5B, PDIA6, PIK3R1, SRGN, SDC2, and RBBP7, and the top up-regulated genes including RPS27A, EEF1A1,
HNRNPA1, CTNNB1, POLR2A, CFL1, CSNk1E, HSPD1, FN1, and AURKB, which can potentially serve as therapeutic
targets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the "Wnt
signaling pathway".
Conclusion: In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modules
using WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslational
modifications. We found nine down-regulated genes and ten up-regulated genes, which could serve as
potential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and cell
adhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm the
effectiveness and safety of targeted interventions.

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与伤口愈合相关的差异表达基因的生物信息学综合分析

目的：伤口愈合是一个复杂的过程，涉及各种基因和分子通路的协调相互作用。本研究旨在发现新的治疗靶点、生物标志物和候选基因，以便开发药物，提高伤口修复干预措施的成功率：本研究是一项网络分析研究。本研究使用了从基因表达总库（GEO）数据库中获得的九个伤口愈合芯片数据集。使用 Limma 软件包描述了差异表达基因（DEGs），并将共享基因作为加权基因共表达网络分析的输入。使用 EnrichR 网络服务器进行了基因本体分析，并通过 STRING 和 Cytoscape 构建了蛋白-蛋白相互作用（PPI）网络：结果：共确定了 424 个 DEGs。结果：共确定了 424 个 DEGs，利用 9 个数据集的 7692 个共有基因构建了共表达网络，从而确定了 7 个模块。在这些模块中，选出了上调和下调幅度最大的 20 个基因。在这些模块中，筛选出了上调和下调幅度最大的 20 个基因，其中下调幅度最大的基因包括 TJP1、SEC61A1、PLEK、ATP5B、PDIA6、PIK3R1、SRGN、SDC2 和 RBBP7，上调幅度最大的基因包括 RPS27A、EEF1A1、HNRNPA1、CTNNB1、POLR2A、CFL1、CSNk1E、HSPD1、FN1 和 AURKB，这些基因有可能成为治疗目标。通过 KEGG 通路分析发现，大部分基因富集在 "Wntsignaling 通路 "中：在对九个伤口愈合芯片数据集的研究中，我们利用 WGCNA 发现了 DEGs 和共表达模块。这些基因参与了转录、翻译和翻译后修饰等重要的细胞过程。我们发现了九个下调基因和十个上调基因，这些基因可能是潜在的治疗靶点，有待进一步的实验验证。靶向与蛋白质合成、细胞粘附和迁移相关的通路可能会促进伤口愈合，但还需要更多的实验验证来确认靶向干预的有效性和安全性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.