Cai-Han Yu, Cai-Xia Wu, Dai Li, Lan-Lan Gong, Xu-Dong Lyu, Jie Yang
{"title":"基于缺氧相关基因的糖尿病视网膜病变关键基因和调控网络：生物信息学分析。","authors":"Cai-Han Yu, Cai-Xia Wu, Dai Li, Lan-Lan Gong, Xu-Dong Lyu, Jie Yang","doi":"10.18240/ijo.2024.08.04","DOIUrl":null,"url":null,"abstract":"<p><strong>Aim: </strong>To prevent neovascularization in diabetic retinopathy (DR) patients and partially control disease progression.</p><p><strong>Methods: </strong>Hypoxia-related differentially expressed genes (DEGs) were identified from the GSE60436 and GSE102485 datasets, followed by gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Potential candidate drugs were screened using the CMap database. Subsequently, a protein-protein interaction (PPI) network was constructed to identify hypoxia-related hub genes. A nomogram was generated using the rms R package, and the correlation of hub genes was analyzed using the Hmisc R package. The clinical significance of hub genes was validated by comparing their expression levels between disease and normal groups and constructing receiver operating characteristic curve (ROC) curves. Finally, a hypoxia-related miRNA-transcription factor (TF)-Hub gene network was constructed using the NetworkAnalyst online tool.</p><p><strong>Results: </strong>Totally 48 hypoxia-related DEGs and screened 10 potential candidate drugs with interaction relationships to upregulated hypoxia-related genes were identified, such as ruxolitinib, meprylcaine, and deferiprone. In addition, 8 hub genes were also identified: glycogen phosphorylase muscle associated (<i>PYGM</i>), glyceraldehyde-3-phosphate dehydrogenase spermatogenic (<i>GAPDHS</i>), enolase 3 (<i>ENO3</i>), aldolase fructose-bisphosphate C (<i>ALDOC</i>), phosphoglucomutase 2 (<i>PGM2</i>), enolase 2 (<i>ENO2</i>), phosphoglycerate mutase 2 (<i>PGAM2</i>), and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (<i>PFKFB3</i>). Based on hub gene predictions, the miRNA-TF-Hub gene network revealed complex interactions between 163 miRNAs, 77 TFs, and hub genes. The results of ROC showed that the except for <i>GAPDHS</i>, the area under curve (AUC) values of the other 7 hub genes were greater than 0.758, indicating their favorable diagnostic performance.</p><p><strong>Conclusion: </strong><i>PYGM</i>, <i>GAPDHS</i>, <i>ENO3</i>, <i>ALDOC</i>, <i>PGM2</i>, <i>ENO2</i>, <i>PGAM2</i>, and <i>PFKFB3</i> are hub genes in DR, and hypoxia-related hub genes exhibited favorable diagnostic performance.</p>","PeriodicalId":14312,"journal":{"name":"International journal of ophthalmology","volume":"17 8","pages":"1411-1417"},"PeriodicalIF":1.9000,"publicationDate":"2024-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286444/pdf/","citationCount":"0","resultStr":"{\"title\":\"Key genes and regulatory networks for diabetic retinopathy based on hypoxia-related genes: a bioinformatics analysis.\",\"authors\":\"Cai-Han Yu, Cai-Xia Wu, Dai Li, Lan-Lan Gong, Xu-Dong Lyu, Jie Yang\",\"doi\":\"10.18240/ijo.2024.08.04\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Aim: </strong>To prevent neovascularization in diabetic retinopathy (DR) patients and partially control disease progression.</p><p><strong>Methods: </strong>Hypoxia-related differentially expressed genes (DEGs) were identified from the GSE60436 and GSE102485 datasets, followed by gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Potential candidate drugs were screened using the CMap database. Subsequently, a protein-protein interaction (PPI) network was constructed to identify hypoxia-related hub genes. A nomogram was generated using the rms R package, and the correlation of hub genes was analyzed using the Hmisc R package. The clinical significance of hub genes was validated by comparing their expression levels between disease and normal groups and constructing receiver operating characteristic curve (ROC) curves. Finally, a hypoxia-related miRNA-transcription factor (TF)-Hub gene network was constructed using the NetworkAnalyst online tool.</p><p><strong>Results: </strong>Totally 48 hypoxia-related DEGs and screened 10 potential candidate drugs with interaction relationships to upregulated hypoxia-related genes were identified, such as ruxolitinib, meprylcaine, and deferiprone. In addition, 8 hub genes were also identified: glycogen phosphorylase muscle associated (<i>PYGM</i>), glyceraldehyde-3-phosphate dehydrogenase spermatogenic (<i>GAPDHS</i>), enolase 3 (<i>ENO3</i>), aldolase fructose-bisphosphate C (<i>ALDOC</i>), phosphoglucomutase 2 (<i>PGM2</i>), enolase 2 (<i>ENO2</i>), phosphoglycerate mutase 2 (<i>PGAM2</i>), and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (<i>PFKFB3</i>). Based on hub gene predictions, the miRNA-TF-Hub gene network revealed complex interactions between 163 miRNAs, 77 TFs, and hub genes. The results of ROC showed that the except for <i>GAPDHS</i>, the area under curve (AUC) values of the other 7 hub genes were greater than 0.758, indicating their favorable diagnostic performance.</p><p><strong>Conclusion: </strong><i>PYGM</i>, <i>GAPDHS</i>, <i>ENO3</i>, <i>ALDOC</i>, <i>PGM2</i>, <i>ENO2</i>, <i>PGAM2</i>, and <i>PFKFB3</i> are hub genes in DR, and hypoxia-related hub genes exhibited favorable diagnostic performance.</p>\",\"PeriodicalId\":14312,\"journal\":{\"name\":\"International journal of ophthalmology\",\"volume\":\"17 8\",\"pages\":\"1411-1417\"},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2024-08-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286444/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International journal of ophthalmology\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.18240/ijo.2024.08.04\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"OPHTHALMOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International journal of ophthalmology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.18240/ijo.2024.08.04","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"OPHTHALMOLOGY","Score":null,"Total":0}
Key genes and regulatory networks for diabetic retinopathy based on hypoxia-related genes: a bioinformatics analysis.
Aim: To prevent neovascularization in diabetic retinopathy (DR) patients and partially control disease progression.
Methods: Hypoxia-related differentially expressed genes (DEGs) were identified from the GSE60436 and GSE102485 datasets, followed by gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Potential candidate drugs were screened using the CMap database. Subsequently, a protein-protein interaction (PPI) network was constructed to identify hypoxia-related hub genes. A nomogram was generated using the rms R package, and the correlation of hub genes was analyzed using the Hmisc R package. The clinical significance of hub genes was validated by comparing their expression levels between disease and normal groups and constructing receiver operating characteristic curve (ROC) curves. Finally, a hypoxia-related miRNA-transcription factor (TF)-Hub gene network was constructed using the NetworkAnalyst online tool.
Results: Totally 48 hypoxia-related DEGs and screened 10 potential candidate drugs with interaction relationships to upregulated hypoxia-related genes were identified, such as ruxolitinib, meprylcaine, and deferiprone. In addition, 8 hub genes were also identified: glycogen phosphorylase muscle associated (PYGM), glyceraldehyde-3-phosphate dehydrogenase spermatogenic (GAPDHS), enolase 3 (ENO3), aldolase fructose-bisphosphate C (ALDOC), phosphoglucomutase 2 (PGM2), enolase 2 (ENO2), phosphoglycerate mutase 2 (PGAM2), and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Based on hub gene predictions, the miRNA-TF-Hub gene network revealed complex interactions between 163 miRNAs, 77 TFs, and hub genes. The results of ROC showed that the except for GAPDHS, the area under curve (AUC) values of the other 7 hub genes were greater than 0.758, indicating their favorable diagnostic performance.
Conclusion: PYGM, GAPDHS, ENO3, ALDOC, PGM2, ENO2, PGAM2, and PFKFB3 are hub genes in DR, and hypoxia-related hub genes exhibited favorable diagnostic performance.
期刊介绍：
· International Journal of Ophthalmology-IJO (English edition) is a global ophthalmological scientific publication
and a peer-reviewed open access periodical (ISSN 2222-3959 print, ISSN 2227-4898 online).
This journal is sponsored by Chinese Medical Association Xi’an Branch and obtains guidance and support from
WHO and ICO (International Council of Ophthalmology). It has been indexed in SCIE, PubMed,
PubMed-Central, Chemical Abstracts, Scopus, EMBASE , and DOAJ. IJO JCR IF in 2017 is 1.166.
IJO was established in 2008, with editorial office in Xi’an, China. It is a monthly publication. General Scientific
Advisors include Prof. Hugh Taylor (President of ICO); Prof.Bruce Spivey (Immediate Past President of ICO);
Prof.Mark Tso (Ex-Vice President of ICO) and Prof.Daiming Fan (Academician and Vice President,
Chinese Academy of Engineering.
International Scientific Advisors include Prof. Serge Resnikoff (WHO Senior Speciatist for Prevention of
blindness), Prof. Chi-Chao Chan (National Eye Institute, USA) and Prof. Richard L Abbott (Ex-President of
AAO/PAAO) et al.
Honorary Editors-in-Chief: Prof. Li-Xin Xie(Academician of Chinese Academy of
Engineering/Honorary President of Chinese Ophthalmological Society); Prof. Dennis Lam (President of APAO) and
Prof. Xiao-Xin Li (Ex-President of Chinese Ophthalmological Society).
Chief Editor: Prof. Xiu-Wen Hu (President of IJO Press).
Editors-in-Chief: Prof. Yan-Nian Hui (Ex-Director, Eye Institute of Chinese PLA) and
Prof. George Chiou (Founding chief editor of Journal of Ocular Pharmacology & Therapeutics).
Associate Editors-in-Chief include:
Prof. Ning-Li Wang (President Elect of APAO);
Prof. Ke Yao (President of Chinese Ophthalmological Society) ;
Prof.William Smiddy (Bascom Palmer Eye instituteUSA) ;
Prof.Joel Schuman (President of Association of University Professors of Ophthalmology,USA);
Prof.Yizhi Liu (Vice President of Chinese Ophtlalmology Society);
Prof.Yu-Sheng Wang (Director of Eye Institute of Chinese PLA);
Prof.Ling-Yun Cheng (Director of Ocular Pharmacology, Shiley Eye Center, USA).
IJO accepts contributions in English from all over the world. It includes mainly original articles and review articles,
both basic and clinical papers.
Instruction is Welcome Contribution is Welcome Citation is Welcome
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International Council of Ophthalmology(ICO), PubMed, PMC, American Academy of Ophthalmology, Asia-Pacific, Thomson Reuters, The Charlesworth Group, Crossref,Scopus,Publons, DOAJ etc.
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