Mansoureh Farhangniya, Farzaneh Mohamadi Farsani, Najmeh Salehi, Ali Samadikuchaksaraei
{"title":"与伤口愈合相关的差异表达基因的生物信息学综合分析","authors":"Mansoureh Farhangniya, Farzaneh Mohamadi Farsani, Najmeh Salehi, Ali Samadikuchaksaraei","doi":"10.22074/cellj.2023.2007217.1368","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>Wound healing is a complex process involving the coordinated interaction of various genes and molecular<br />pathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug development<br />to improve successful wound repair interventions.<br />Materials and Methods: This study is a network-meta analysis study. Nine wound healing microarray datasets obtained<br />from the Gene Expression Omnibus (GEO) database were used for this study. Differentially expressed genes (DEGs)<br />were described using the Limma package and shared genes were used as input for weighted gene co-expression<br />network analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of a<br />protein-protein interaction (PPI) network was achieved by the STRING and Cytoscape.<br />Results: A total of 424 DEGs were determined. A co-expression network was constructed using 7692 shared genes<br />between nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20<br />genes of up and down-regulation were selected. The top down-regulated genes, including TJP1, SEC61A1, PLEK,<br />ATP5B, PDIA6, PIK3R1, SRGN, SDC2, and RBBP7, and the top up-regulated genes including RPS27A, EEF1A1,<br />HNRNPA1, CTNNB1, POLR2A, CFL1, CSNk1E, HSPD1, FN1, and AURKB, which can potentially serve as therapeutic<br />targets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the \"Wnt<br />signaling pathway\".<br />Conclusion: In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modules<br />using WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslational<br />modifications. We found nine down-regulated genes and ten up-regulated genes, which could serve as<br />potential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and cell<br />adhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm the<br />effectiveness and safety of targeted interventions.</p>","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":null,"pages":null},"PeriodicalIF":16.4000,"publicationDate":"2023-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10777322/pdf/","citationCount":"0","resultStr":"{\"title\":\"Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing.\",\"authors\":\"Mansoureh Farhangniya, Farzaneh Mohamadi Farsani, Najmeh Salehi, Ali Samadikuchaksaraei\",\"doi\":\"10.22074/cellj.2023.2007217.1368\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Objective: </strong>Wound healing is a complex process involving the coordinated interaction of various genes and molecular<br />pathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug development<br />to improve successful wound repair interventions.<br />Materials and Methods: This study is a network-meta analysis study. Nine wound healing microarray datasets obtained<br />from the Gene Expression Omnibus (GEO) database were used for this study. Differentially expressed genes (DEGs)<br />were described using the Limma package and shared genes were used as input for weighted gene co-expression<br />network analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of a<br />protein-protein interaction (PPI) network was achieved by the STRING and Cytoscape.<br />Results: A total of 424 DEGs were determined. A co-expression network was constructed using 7692 shared genes<br />between nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20<br />genes of up and down-regulation were selected. The top down-regulated genes, including TJP1, SEC61A1, PLEK,<br />ATP5B, PDIA6, PIK3R1, SRGN, SDC2, and RBBP7, and the top up-regulated genes including RPS27A, EEF1A1,<br />HNRNPA1, CTNNB1, POLR2A, CFL1, CSNk1E, HSPD1, FN1, and AURKB, which can potentially serve as therapeutic<br />targets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the \\\"Wnt<br />signaling pathway\\\".<br />Conclusion: In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modules<br />using WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslational<br />modifications. We found nine down-regulated genes and ten up-regulated genes, which could serve as<br />potential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and cell<br />adhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm the<br />effectiveness and safety of targeted interventions.</p>\",\"PeriodicalId\":1,\"journal\":{\"name\":\"Accounts of Chemical Research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":16.4000,\"publicationDate\":\"2023-12-31\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10777322/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Accounts of Chemical Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.22074/cellj.2023.2007217.1368\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Accounts of Chemical Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.22074/cellj.2023.2007217.1368","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing.
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.
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.
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