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Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor
BACKGROUND: Wilms tumor is the most common childhood kidney malignant tumor. However, the genes and signaling pathways associated with the disease remain incompletely understood. METHODS: GSE66405, GSE73209, and GSE11151 were collected from the Gene Expression Omnibus (GEO) database, and differentia...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
AME Publishing Company
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9459508/ https://www.ncbi.nlm.nih.gov/pubmed/36093523 http://dx.doi.org/10.21037/tcr-22-1847 |
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author | Li, Yufeng Tang, Haizhou Huang, Zhenwen Qin, Huaxing Cen, Qin Meng, Fei Huang, Liang Lin, Lifang Pu, Jian Yang, Di |
author_facet | Li, Yufeng Tang, Haizhou Huang, Zhenwen Qin, Huaxing Cen, Qin Meng, Fei Huang, Liang Lin, Lifang Pu, Jian Yang, Di |
author_sort | Li, Yufeng |
collection | PubMed |
description | BACKGROUND: Wilms tumor is the most common childhood kidney malignant tumor. However, the genes and signaling pathways associated with the disease remain incompletely understood. METHODS: GSE66405, GSE73209, and GSE11151 were collected from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were detected using R software. A protein-protein interaction (PPI) network was constructed using the STRING database, and the clustering modules and hub genes were analyzed with the Cytoscape software. Genes functional enrichment analyses were performed using the package “clusterProfiler” in R software, and the gene set enrichment analysis (GSEA) analysis was performed using GSEA v4.1.0 software. RESULTS: Respectively, 3,092, 620, and 3,567 DEGs were screened in GSE66405, GSE73209, and GSE11151, with a total of 474 common DEGs detected in three expression profiles. For the common DEGs, the top 30 significant results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were presented. Furthermore, five modules were found as the most related modules to Wilms tumor. GO term and KEGG pathway enrichment analyses of the genes in all the modules identified 10 GO terms and 5 KEGG pathways as significantly enriched. The top 10 hub DEGs of the PPI network were ALB, CDH1, EGF, AQP2, REN, SLC2A2, SPP1, UMOD, NPHS2, and FOXM1, with ALB identified as the highest degree. GSEA results showed 11 pathways were correlated with ALB expression in GSE66405 and 10 pathways were related to the expression of the ALB gene in GSE73209. CONCLUSIONS: Our study revealed robust gene signatures in Wilms tumor. Dysregulations of the signaling pathways were associated with the development and progression of the Wilms tumor, and 10 hub genes may play important roles in its diagnosis and therapy. |
format | Online Article Text |
id | pubmed-9459508 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | AME Publishing Company |
record_format | MEDLINE/PubMed |
spelling | pubmed-94595082022-09-10 Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor Li, Yufeng Tang, Haizhou Huang, Zhenwen Qin, Huaxing Cen, Qin Meng, Fei Huang, Liang Lin, Lifang Pu, Jian Yang, Di Transl Cancer Res Original Article BACKGROUND: Wilms tumor is the most common childhood kidney malignant tumor. However, the genes and signaling pathways associated with the disease remain incompletely understood. METHODS: GSE66405, GSE73209, and GSE11151 were collected from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were detected using R software. A protein-protein interaction (PPI) network was constructed using the STRING database, and the clustering modules and hub genes were analyzed with the Cytoscape software. Genes functional enrichment analyses were performed using the package “clusterProfiler” in R software, and the gene set enrichment analysis (GSEA) analysis was performed using GSEA v4.1.0 software. RESULTS: Respectively, 3,092, 620, and 3,567 DEGs were screened in GSE66405, GSE73209, and GSE11151, with a total of 474 common DEGs detected in three expression profiles. For the common DEGs, the top 30 significant results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were presented. Furthermore, five modules were found as the most related modules to Wilms tumor. GO term and KEGG pathway enrichment analyses of the genes in all the modules identified 10 GO terms and 5 KEGG pathways as significantly enriched. The top 10 hub DEGs of the PPI network were ALB, CDH1, EGF, AQP2, REN, SLC2A2, SPP1, UMOD, NPHS2, and FOXM1, with ALB identified as the highest degree. GSEA results showed 11 pathways were correlated with ALB expression in GSE66405 and 10 pathways were related to the expression of the ALB gene in GSE73209. CONCLUSIONS: Our study revealed robust gene signatures in Wilms tumor. Dysregulations of the signaling pathways were associated with the development and progression of the Wilms tumor, and 10 hub genes may play important roles in its diagnosis and therapy. AME Publishing Company 2022-08 /pmc/articles/PMC9459508/ /pubmed/36093523 http://dx.doi.org/10.21037/tcr-22-1847 Text en 2022 Translational Cancer Research. All rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0 (https://creativecommons.org/licenses/by-nc-nd/4.0/) . |
spellingShingle | Original Article Li, Yufeng Tang, Haizhou Huang, Zhenwen Qin, Huaxing Cen, Qin Meng, Fei Huang, Liang Lin, Lifang Pu, Jian Yang, Di Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor |
title | Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor |
title_full | Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor |
title_fullStr | Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor |
title_full_unstemmed | Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor |
title_short | Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor |
title_sort | bioinformatics analysis and identification of genes and pathways involved in patients with wilms tumor |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9459508/ https://www.ncbi.nlm.nih.gov/pubmed/36093523 http://dx.doi.org/10.21037/tcr-22-1847 |
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