Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma

Ping Ouyang; Wenyan Wu; Rang Li; Xuefeng Zhou; Tao Li

doi:doi:10.11648/j.ajim.20210901.16

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Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma

Ping Ouyang, Wenyan Wu, Rang Li, Xuefeng Zhou, Tao Li

Published in American Journal of Internal Medicine (Volume 9, Issue 1)

Received: 5 January 2021 Accepted: 22 January 2021 Published: 28 January 2021

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Abstract

Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and miR-sequencing data were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. Then, the gene function annotations about the DEGs were predicted using Gene Ontology (GO) and KEGG pathway. Subsequently, the protein-protein interaction (PPI) network was established based on the STRING database, and function modules were identified using Cytoscape. Finally, DEGs targeted by DEMs were predicted by using the miRDB, miRTarBase, TargetScan and DIANA databases, and the DEM-DEG negative interaction network was built. Results: In all, 704 DEGs (about 49.9% upregulated) were enriched in 234 GO terms and 53 KEGG pathways. Seven hub genes (APP, GNG2, VAV1, RAC2, YES1, EGFR and GNB5) in 6 function modules were found for the PPI network. In addition, 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, moreover, these pairs may potentially contributed to NPC pathogenesis. Conclusion: The constructed miRNA-mRNA negetive regulatory network will give help in elucidating the molecular mechanisms of NPC. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future.

Published in	American Journal of Internal Medicine (Volume 9, Issue 1)
DOI	10.11648/j.ajim.20210901.16
Page(s)	36-48
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Nasopharyngeal Carcinoma (NPC), Differentially Expressed Genes (DEGs), Differentially Expressed microRNAs (DEMs), miRNA-mRNA Regulatory Network

References

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APA Style

Ping Ouyang, Wenyan Wu, Rang Li, Xuefeng Zhou, Tao Li. (2021). Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma. American Journal of Internal Medicine, 9(1), 36-48. https://doi.org/10.11648/j.ajim.20210901.16

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ACS Style

Ping Ouyang; Wenyan Wu; Rang Li; Xuefeng Zhou; Tao Li. Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma. Am. J. Intern. Med. 2021, 9(1), 36-48. doi: 10.11648/j.ajim.20210901.16

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AMA Style

Ping Ouyang, Wenyan Wu, Rang Li, Xuefeng Zhou, Tao Li. Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma. Am J Intern Med. 2021;9(1):36-48. doi: 10.11648/j.ajim.20210901.16

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@article{10.11648/j.ajim.20210901.16,
  author = {Ping Ouyang and Wenyan Wu and Rang Li and Xuefeng Zhou and Tao Li},
  title = {Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma},
  journal = {American Journal of Internal Medicine},
  volume = {9},
  number = {1},
  pages = {36-48},
  doi = {10.11648/j.ajim.20210901.16},
  url = {https://doi.org/10.11648/j.ajim.20210901.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajim.20210901.16},
  abstract = {Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and miR-sequencing data were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. Then, the gene function annotations about the DEGs were predicted using Gene Ontology (GO) and KEGG pathway. Subsequently, the protein-protein interaction (PPI) network was established based on the STRING database, and function modules were identified using Cytoscape. Finally, DEGs targeted by DEMs were predicted by using the miRDB, miRTarBase, TargetScan and DIANA databases, and the DEM-DEG negative interaction network was built. Results: In all, 704 DEGs (about 49.9% upregulated) were enriched in 234 GO terms and 53 KEGG pathways. Seven hub genes (APP, GNG2, VAV1, RAC2, YES1, EGFR and GNB5) in 6 function modules were found for the PPI network. In addition, 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, moreover, these pairs may potentially contributed to NPC pathogenesis. Conclusion: The constructed miRNA-mRNA negetive regulatory network will give help in elucidating the molecular mechanisms of NPC. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future.},
 year = {2021}
}

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TY  - JOUR
T1  - Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma
AU  - Ping Ouyang
AU  - Wenyan Wu
AU  - Rang Li
AU  - Xuefeng Zhou
AU  - Tao Li
Y1  - 2021/01/28
PY  - 2021
N1  - https://doi.org/10.11648/j.ajim.20210901.16
DO  - 10.11648/j.ajim.20210901.16
T2  - American Journal of Internal Medicine
JF  - American Journal of Internal Medicine
JO  - American Journal of Internal Medicine
SP  - 36
EP  - 48
PB  - Science Publishing Group
SN  - 2330-4324
UR  - https://doi.org/10.11648/j.ajim.20210901.16
AB  - Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and miR-sequencing data were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. Then, the gene function annotations about the DEGs were predicted using Gene Ontology (GO) and KEGG pathway. Subsequently, the protein-protein interaction (PPI) network was established based on the STRING database, and function modules were identified using Cytoscape. Finally, DEGs targeted by DEMs were predicted by using the miRDB, miRTarBase, TargetScan and DIANA databases, and the DEM-DEG negative interaction network was built. Results: In all, 704 DEGs (about 49.9% upregulated) were enriched in 234 GO terms and 53 KEGG pathways. Seven hub genes (APP, GNG2, VAV1, RAC2, YES1, EGFR and GNB5) in 6 function modules were found for the PPI network. In addition, 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, moreover, these pairs may potentially contributed to NPC pathogenesis. Conclusion: The constructed miRNA-mRNA negetive regulatory network will give help in elucidating the molecular mechanisms of NPC. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future.
VL  - 9
IS  - 1
ER  -

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Author Information

Ping Ouyang

Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, P. R. China
Wenyan Wu

Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, P. R. China
Rang Li

Institute of Medical Systems Biology, School of Public Health, Guangdong Medical University, Dongguan, P. R. China
Xuefeng Zhou

Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, P. R. China
Tao Li

Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, P. R. China

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Plain Text BibTeX RIS

APA Style

Ping Ouyang, Wenyan Wu, Rang Li, Xuefeng Zhou, Tao Li. (2021). Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma. American Journal of Internal Medicine, 9(1), 36-48. https://doi.org/10.11648/j.ajim.20210901.16

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ACS Style

Ping Ouyang; Wenyan Wu; Rang Li; Xuefeng Zhou; Tao Li. Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma. Am. J. Intern. Med. 2021, 9(1), 36-48. doi: 10.11648/j.ajim.20210901.16

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AMA Style

Ping Ouyang, Wenyan Wu, Rang Li, Xuefeng Zhou, Tao Li. Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma. Am J Intern Med. 2021;9(1):36-48. doi: 10.11648/j.ajim.20210901.16

Copy | Download

@article{10.11648/j.ajim.20210901.16,
  author = {Ping Ouyang and Wenyan Wu and Rang Li and Xuefeng Zhou and Tao Li},
  title = {Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma},
  journal = {American Journal of Internal Medicine},
  volume = {9},
  number = {1},
  pages = {36-48},
  doi = {10.11648/j.ajim.20210901.16},
  url = {https://doi.org/10.11648/j.ajim.20210901.16},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajim.20210901.16},
  abstract = {Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and miR-sequencing data were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. Then, the gene function annotations about the DEGs were predicted using Gene Ontology (GO) and KEGG pathway. Subsequently, the protein-protein interaction (PPI) network was established based on the STRING database, and function modules were identified using Cytoscape. Finally, DEGs targeted by DEMs were predicted by using the miRDB, miRTarBase, TargetScan and DIANA databases, and the DEM-DEG negative interaction network was built. Results: In all, 704 DEGs (about 49.9% upregulated) were enriched in 234 GO terms and 53 KEGG pathways. Seven hub genes (APP, GNG2, VAV1, RAC2, YES1, EGFR and GNB5) in 6 function modules were found for the PPI network. In addition, 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, moreover, these pairs may potentially contributed to NPC pathogenesis. Conclusion: The constructed miRNA-mRNA negetive regulatory network will give help in elucidating the molecular mechanisms of NPC. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future.},
 year = {2021}
}

Copy | Download

TY  - JOUR
T1  - Analysis of the Differentially Expressed Genes and microRNAs and Prediction of miRNA-mRNA negative Regulatory Network in Nasopharyngeal Carcinoma
AU  - Ping Ouyang
AU  - Wenyan Wu
AU  - Rang Li
AU  - Xuefeng Zhou
AU  - Tao Li
Y1  - 2021/01/28
PY  - 2021
N1  - https://doi.org/10.11648/j.ajim.20210901.16
DO  - 10.11648/j.ajim.20210901.16
T2  - American Journal of Internal Medicine
JF  - American Journal of Internal Medicine
JO  - American Journal of Internal Medicine
SP  - 36
EP  - 48
PB  - Science Publishing Group
SN  - 2330-4324
UR  - https://doi.org/10.11648/j.ajim.20210901.16
AB  - Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and miR-sequencing data were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. Then, the gene function annotations about the DEGs were predicted using Gene Ontology (GO) and KEGG pathway. Subsequently, the protein-protein interaction (PPI) network was established based on the STRING database, and function modules were identified using Cytoscape. Finally, DEGs targeted by DEMs were predicted by using the miRDB, miRTarBase, TargetScan and DIANA databases, and the DEM-DEG negative interaction network was built. Results: In all, 704 DEGs (about 49.9% upregulated) were enriched in 234 GO terms and 53 KEGG pathways. Seven hub genes (APP, GNG2, VAV1, RAC2, YES1, EGFR and GNB5) in 6 function modules were found for the PPI network. In addition, 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, moreover, these pairs may potentially contributed to NPC pathogenesis. Conclusion: The constructed miRNA-mRNA negetive regulatory network will give help in elucidating the molecular mechanisms of NPC. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future.
VL  - 9
IS  - 1
ER  -

Copy | Download