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Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma
AIM: The current study analyzed the miRNA microarray dataset (GSE66274) and gene expression microarray dataset (GSE38129) with similar samples to achieve a better understanding of miRNA-mRNA interactions. BACKGROUND: The most common form of esophageal cancer is esophageal squamous cell carcinoma (ES...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Shaheed Beheshti University of Medical Sciences
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9589132/ https://www.ncbi.nlm.nih.gov/pubmed/36311956 http://dx.doi.org/10.22037/ghfbb.v15i3.2465 |
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author | Askari, Nahid Hadizadeh, Morteza |
author_facet | Askari, Nahid Hadizadeh, Morteza |
author_sort | Askari, Nahid |
collection | PubMed |
description | AIM: The current study analyzed the miRNA microarray dataset (GSE66274) and gene expression microarray dataset (GSE38129) with similar samples to achieve a better understanding of miRNA-mRNA interactions. BACKGROUND: The most common form of esophageal cancer is esophageal squamous cell carcinoma (ESCC). While, miRNAs are well recognized as having a critical regulatory role in human cancer, their responsibilities and mechanisms of miRNA-mRNA in ESCC are unknown. METHODS: Differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) were identified using the LIMMA package in R. In total, 478 DEmRNA (224 upregulated and 254 downregulated) and 39 DEmiRNA (15 upregulated and 24 downregulated) were screened. The RNAInter database analyzed miRNA-mRNA interactions; then, the miRNA-mRNA network was visualized by Cytoscape software. ClusterProfiler packages were used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEmRNA as targets of DEmiRNAs. RESULTS: KEGG pathway analysis indicated that the p53 signaling pathway, ECM−receptor interaction, and AGE−RAGE signaling pathway were significant. Cellular response to amino acid stimulus, negative regulation of apoptotic signaling pathway, and endoderm formation were most prevalent in the biological process category. Additionally, the collagen−containing extracellular matrix, actomyosin complex collagen trimers, basement membrane, and extracellular matrix structural constituent were more enriched. CONCLUSION: Overall, the present survey provides evidence that could support the prognosis of esophageal tumors in the future. |
format | Online Article Text |
id | pubmed-9589132 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Shaheed Beheshti University of Medical Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-95891322022-10-28 Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma Askari, Nahid Hadizadeh, Morteza Gastroenterol Hepatol Bed Bench Original Article AIM: The current study analyzed the miRNA microarray dataset (GSE66274) and gene expression microarray dataset (GSE38129) with similar samples to achieve a better understanding of miRNA-mRNA interactions. BACKGROUND: The most common form of esophageal cancer is esophageal squamous cell carcinoma (ESCC). While, miRNAs are well recognized as having a critical regulatory role in human cancer, their responsibilities and mechanisms of miRNA-mRNA in ESCC are unknown. METHODS: Differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) were identified using the LIMMA package in R. In total, 478 DEmRNA (224 upregulated and 254 downregulated) and 39 DEmiRNA (15 upregulated and 24 downregulated) were screened. The RNAInter database analyzed miRNA-mRNA interactions; then, the miRNA-mRNA network was visualized by Cytoscape software. ClusterProfiler packages were used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEmRNA as targets of DEmiRNAs. RESULTS: KEGG pathway analysis indicated that the p53 signaling pathway, ECM−receptor interaction, and AGE−RAGE signaling pathway were significant. Cellular response to amino acid stimulus, negative regulation of apoptotic signaling pathway, and endoderm formation were most prevalent in the biological process category. Additionally, the collagen−containing extracellular matrix, actomyosin complex collagen trimers, basement membrane, and extracellular matrix structural constituent were more enriched. CONCLUSION: Overall, the present survey provides evidence that could support the prognosis of esophageal tumors in the future. Shaheed Beheshti University of Medical Sciences 2022 /pmc/articles/PMC9589132/ /pubmed/36311956 http://dx.doi.org/10.22037/ghfbb.v15i3.2465 Text en ©2022 RIGLD, Research Institute for Gastroenterology and Liver Diseases https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article, distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/) which permits others to copy and redistribute the material just in noncommercial usages, provided the original work is properly cited. |
spellingShingle | Original Article Askari, Nahid Hadizadeh, Morteza Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma |
title | Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma |
title_full | Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma |
title_fullStr | Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma |
title_full_unstemmed | Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma |
title_short | Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma |
title_sort | bioinformatics-based identification of mirnas, mrna, and regulatory signaling pathways involved in esophageal squamous cell carcinoma |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9589132/ https://www.ncbi.nlm.nih.gov/pubmed/36311956 http://dx.doi.org/10.22037/ghfbb.v15i3.2465 |
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