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 molecularpathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug developmentto improve successful wound repair interventions.Materials and Methods:...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Royan Institute (ACECR), Tehran
2023-12-01
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| Series: | Cell Journal |
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| Online Access: | https://www.celljournal.org/article_708782_827696033e69a431846efefd5e2c415f.pdf |
| _version_ | 1797359935161368576 |
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| author | Mansoureh Farhangniya Farzaneh Mohamadi Farsani Najmeh Salehi Ali Samadikuchaksaraei |
| author_facet | Mansoureh Farhangniya Farzaneh Mohamadi Farsani Najmeh Salehi Ali Samadikuchaksaraei |
| author_sort | Mansoureh Farhangniya |
| collection | DOAJ |
| description | Objective: Wound healing is a complex process involving the coordinated interaction of various genes and molecularpathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug developmentto improve successful wound repair interventions.Materials and Methods: This study is a network-meta analysis study. Nine wound healing microarray datasets obtainedfrom 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-expressionnetwork analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of aprotein-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 genesbetween nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20genes 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 therapeutictargets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the "Wntsignaling pathway".Conclusion: In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modulesusing WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslationalmodifications. We found nine down-regulated genes and ten up-regulated genes, which could serve aspotential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and celladhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm theeffectiveness and safety of targeted interventions. |
| first_indexed | 2024-03-08T15:31:07Z |
| format | Article |
| id | doaj.art-e259ef2953ff45a6959226f4169f2222 |
| institution | Directory Open Access Journal |
| issn | 2228-5806 2228-5814 |
| language | English |
| last_indexed | 2024-03-08T15:31:07Z |
| publishDate | 2023-12-01 |
| publisher | Royan Institute (ACECR), Tehran |
| record_format | Article |
| series | Cell Journal |
| spelling | doaj.art-e259ef2953ff45a6959226f4169f22222024-01-10T05:28:27ZengRoyan Institute (ACECR), TehranCell Journal2228-58062228-58142023-12-01251287488210.22074/cellj.2023.2007217.1368708782Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound HealingMansoureh Farhangniya0Farzaneh Mohamadi Farsani1Najmeh Salehi2Ali Samadikuchaksaraei3Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, IranDepartment of Biology, Naghshejahan Higher Education Institute, Isfahan, IranSchool of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, IranDepartment of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, IranObjective: Wound healing is a complex process involving the coordinated interaction of various genes and molecularpathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug developmentto improve successful wound repair interventions.Materials and Methods: This study is a network-meta analysis study. Nine wound healing microarray datasets obtainedfrom 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-expressionnetwork analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of aprotein-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 genesbetween nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20genes 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 therapeutictargets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the "Wntsignaling pathway".Conclusion: In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modulesusing WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslationalmodifications. We found nine down-regulated genes and ten up-regulated genes, which could serve aspotential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and celladhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm theeffectiveness and safety of targeted interventions.https://www.celljournal.org/article_708782_827696033e69a431846efefd5e2c415f.pdfbioinformaticsgenenetwork-meta analysisregenerationwound healing |
| spellingShingle | Mansoureh Farhangniya Farzaneh Mohamadi Farsani Najmeh Salehi Ali Samadikuchaksaraei Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing Cell Journal bioinformatics gene network-meta analysis regeneration wound healing |
| title | Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing |
| title_full | Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing |
| title_fullStr | Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing |
| title_full_unstemmed | Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing |
| title_short | Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing |
| title_sort | integrated bioinformatic analysis of differentially expressed genes associated with wound healing |
| topic | bioinformatics gene network-meta analysis regeneration wound healing |
| url | https://www.celljournal.org/article_708782_827696033e69a431846efefd5e2c415f.pdf |
| work_keys_str_mv | AT mansourehfarhangniya integratedbioinformaticanalysisofdifferentiallyexpressedgenesassociatedwithwoundhealing AT farzanehmohamadifarsani integratedbioinformaticanalysisofdifferentiallyexpressedgenesassociatedwithwoundhealing AT najmehsalehi integratedbioinformaticanalysisofdifferentiallyexpressedgenesassociatedwithwoundhealing AT alisamadikuchaksaraei integratedbioinformaticanalysisofdifferentiallyexpressedgenesassociatedwithwoundhealing |