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ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics
BACKGROUND: The aim of this study is to investigate the genetic and epigenetic mechanisms involved in the pathogenesis of age-related cataract (ARC). METHODS: We obtained the transcriptome datafile of th ree ARC samples and three healthy, age-matched samples and used differential expression analyses...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10040182/ https://www.ncbi.nlm.nih.gov/pubmed/36987450 http://dx.doi.org/10.7717/peerj.15054 |
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author | Hong, Yingying Wu, Jiawen Sun, Yang Zhang, Shenghai Lu, Yi Ji, Yinghong |
author_facet | Hong, Yingying Wu, Jiawen Sun, Yang Zhang, Shenghai Lu, Yi Ji, Yinghong |
author_sort | Hong, Yingying |
collection | PubMed |
description | BACKGROUND: The aim of this study is to investigate the genetic and epigenetic mechanisms involved in the pathogenesis of age-related cataract (ARC). METHODS: We obtained the transcriptome datafile of th ree ARC samples and three healthy, age-matched samples and used differential expression analyses to identify the differentially expressed genes (DEGs). The differential lncRNA-associated competing endogenous (ceRNA) network, and the protein-protein network (PPI) were constructed using Cytoscape and STRING. Cluster analyses were performed to identify the underlying molecular mechanisms of the hub genes affecting ARC progression. To verify the immune status of the ARC patients, immune-associated analyses were also conducted. RESULTS: The PPI network identified the FOXO1 gene as the hub gene with the highest score, as calculated by the Maximal Clique Centrality (MCC) algorithm. The ceRNA network identified lncRNAs H19, XIST, TTTY14, and MEG3 and hub genes FOXO1, NOTCH3, CDK6, SPRY2, and CA2 as playing key roles in regulating the pathogenesis of ARC. Additionally, the identified hub genes showed no significant correlation with an immune response but were highly correlated with cell metabolism, including cysteine, methionine, and galactose. DISCUSSION: The findings of this study may provide clues toward ARC pathogenic mechanisms and may be of significance for future therapeutic research. |
format | Online Article Text |
id | pubmed-10040182 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-100401822023-03-27 ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics Hong, Yingying Wu, Jiawen Sun, Yang Zhang, Shenghai Lu, Yi Ji, Yinghong PeerJ Bioinformatics BACKGROUND: The aim of this study is to investigate the genetic and epigenetic mechanisms involved in the pathogenesis of age-related cataract (ARC). METHODS: We obtained the transcriptome datafile of th ree ARC samples and three healthy, age-matched samples and used differential expression analyses to identify the differentially expressed genes (DEGs). The differential lncRNA-associated competing endogenous (ceRNA) network, and the protein-protein network (PPI) were constructed using Cytoscape and STRING. Cluster analyses were performed to identify the underlying molecular mechanisms of the hub genes affecting ARC progression. To verify the immune status of the ARC patients, immune-associated analyses were also conducted. RESULTS: The PPI network identified the FOXO1 gene as the hub gene with the highest score, as calculated by the Maximal Clique Centrality (MCC) algorithm. The ceRNA network identified lncRNAs H19, XIST, TTTY14, and MEG3 and hub genes FOXO1, NOTCH3, CDK6, SPRY2, and CA2 as playing key roles in regulating the pathogenesis of ARC. Additionally, the identified hub genes showed no significant correlation with an immune response but were highly correlated with cell metabolism, including cysteine, methionine, and galactose. DISCUSSION: The findings of this study may provide clues toward ARC pathogenic mechanisms and may be of significance for future therapeutic research. PeerJ Inc. 2023-03-23 /pmc/articles/PMC10040182/ /pubmed/36987450 http://dx.doi.org/10.7717/peerj.15054 Text en ©2023 Hong et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics Hong, Yingying Wu, Jiawen Sun, Yang Zhang, Shenghai Lu, Yi Ji, Yinghong ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics |
title | ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics |
title_full | ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics |
title_fullStr | ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics |
title_full_unstemmed | ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics |
title_short | ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics |
title_sort | cerna network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10040182/ https://www.ncbi.nlm.nih.gov/pubmed/36987450 http://dx.doi.org/10.7717/peerj.15054 |
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