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Investigation of hub genes involved in Turner syndrome using biological informatics methods

BACKGROUND: This study aimed to explore candidate genes and their potential interaction mechanism critical to the pathophysiology of Turner syndrome by using the Gene Expression Omnibus database. METHODS: GSE58435 data set was obtained by querying the Gene Expression Omnibus database. Differentially...

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Autores principales: Cheng, Tiantian, Li, Xiaoli, Chen, Jinhu, Yang, Linlin, Liu, Jing, Song, Guangyao, Ma, Huijuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Lippincott Williams & Wilkins 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10684194/
https://www.ncbi.nlm.nih.gov/pubmed/35356930
http://dx.doi.org/10.1097/MD.0000000000029069
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author Cheng, Tiantian
Li, Xiaoli
Chen, Jinhu
Yang, Linlin
Liu, Jing
Song, Guangyao
Ma, Huijuan
author_facet Cheng, Tiantian
Li, Xiaoli
Chen, Jinhu
Yang, Linlin
Liu, Jing
Song, Guangyao
Ma, Huijuan
author_sort Cheng, Tiantian
collection PubMed
description BACKGROUND: This study aimed to explore candidate genes and their potential interaction mechanism critical to the pathophysiology of Turner syndrome by using the Gene Expression Omnibus database. METHODS: GSE58435 data set was obtained by querying the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using R and subsequently annotated by Gene Ontology. Functional enrichment analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes database for annotation, visualization, and integrated discovery. A protein-protein interaction network of different genes was constructed based on the STRING database, in which hub genes were explored through Cytoscape software. The expression of the hub genes was verified by analyzing the gene expression in the GSE46687 data set. RESULTS: A total of 733 differential genes were identified. These differentially expressed genes were significantly enriched in nucleoplasm and nucleus. Their molecular function was concentrated on DNA binding and transcription, coronary artery, and adipose tissue development. According to the annotation of Kyoto Encyclopedia of Genes and Genomes, the identified DEGs were mainly enriched in inflammatory mediator regulation of TRP channels, osteoclast differentiation. A total of 10 hub genes (HIST1H2BA, TRIM71, HIST1H2BB, HIST1H4D, TNF, TP53BP1, CDCA8, EGF, HMG20B, and BCL9) were identified from the constructed protein-protein interaction network. These genes were discovered to be highly expressed in osteoclasts, ovaries, digestive tract, blood, and lymphatic tissues through the online application of human protein atlas. CONCLUSION: In this study, 733 DEGs and 10 hub genes were identified. They would be new candidate targets in Turner syndrome.
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spelling pubmed-106841942023-11-30 Investigation of hub genes involved in Turner syndrome using biological informatics methods Cheng, Tiantian Li, Xiaoli Chen, Jinhu Yang, Linlin Liu, Jing Song, Guangyao Ma, Huijuan Medicine (Baltimore) Clinical Trial/Experimental Study BACKGROUND: This study aimed to explore candidate genes and their potential interaction mechanism critical to the pathophysiology of Turner syndrome by using the Gene Expression Omnibus database. METHODS: GSE58435 data set was obtained by querying the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened using R and subsequently annotated by Gene Ontology. Functional enrichment analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes database for annotation, visualization, and integrated discovery. A protein-protein interaction network of different genes was constructed based on the STRING database, in which hub genes were explored through Cytoscape software. The expression of the hub genes was verified by analyzing the gene expression in the GSE46687 data set. RESULTS: A total of 733 differential genes were identified. These differentially expressed genes were significantly enriched in nucleoplasm and nucleus. Their molecular function was concentrated on DNA binding and transcription, coronary artery, and adipose tissue development. According to the annotation of Kyoto Encyclopedia of Genes and Genomes, the identified DEGs were mainly enriched in inflammatory mediator regulation of TRP channels, osteoclast differentiation. A total of 10 hub genes (HIST1H2BA, TRIM71, HIST1H2BB, HIST1H4D, TNF, TP53BP1, CDCA8, EGF, HMG20B, and BCL9) were identified from the constructed protein-protein interaction network. These genes were discovered to be highly expressed in osteoclasts, ovaries, digestive tract, blood, and lymphatic tissues through the online application of human protein atlas. CONCLUSION: In this study, 733 DEGs and 10 hub genes were identified. They would be new candidate targets in Turner syndrome. Lippincott Williams & Wilkins 2022-03-18 /pmc/articles/PMC10684194/ /pubmed/35356930 http://dx.doi.org/10.1097/MD.0000000000029069 Text en Copyright © 2022 the Author(s). Published by Wolters Kluwer Health, Inc. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY) (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Clinical Trial/Experimental Study
Cheng, Tiantian
Li, Xiaoli
Chen, Jinhu
Yang, Linlin
Liu, Jing
Song, Guangyao
Ma, Huijuan
Investigation of hub genes involved in Turner syndrome using biological informatics methods
title Investigation of hub genes involved in Turner syndrome using biological informatics methods
title_full Investigation of hub genes involved in Turner syndrome using biological informatics methods
title_fullStr Investigation of hub genes involved in Turner syndrome using biological informatics methods
title_full_unstemmed Investigation of hub genes involved in Turner syndrome using biological informatics methods
title_short Investigation of hub genes involved in Turner syndrome using biological informatics methods
title_sort investigation of hub genes involved in turner syndrome using biological informatics methods
topic Clinical Trial/Experimental Study
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10684194/
https://www.ncbi.nlm.nih.gov/pubmed/35356930
http://dx.doi.org/10.1097/MD.0000000000029069
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