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Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis

PURPOSE: Oral squamous cell carcinoma (OSCC) is one of the most common malignant diseases worldwide, yet its molecular mechanisms are largely unknown. We aimed to construct gene co-expression networks to identify key modules and hub genes involved in the pathogenesis of OSCC. PATIENTS AND METHODS: W...

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Autores principales: Zhang, Xiaoqi, Feng, Hao, Li, Ziyu, Li, Dongfang, Liu, Shanshan, Huang, Haiyun, Li, Minqi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Dove Medical Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157991/
https://www.ncbi.nlm.nih.gov/pubmed/30275705
http://dx.doi.org/10.2147/OTT.S171791
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author Zhang, Xiaoqi
Feng, Hao
Li, Ziyu
Li, Dongfang
Liu, Shanshan
Huang, Haiyun
Li, Minqi
author_facet Zhang, Xiaoqi
Feng, Hao
Li, Ziyu
Li, Dongfang
Liu, Shanshan
Huang, Haiyun
Li, Minqi
author_sort Zhang, Xiaoqi
collection PubMed
description PURPOSE: Oral squamous cell carcinoma (OSCC) is one of the most common malignant diseases worldwide, yet its molecular mechanisms are largely unknown. We aimed to construct gene co-expression networks to identify key modules and hub genes involved in the pathogenesis of OSCC. PATIENTS AND METHODS: We used dataset GSE30784 to construct co-expression networks by weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by Database for Annotation, Visualization and Integrated Discovery (DAVID). Hub genes were screened and validated by other datasets. RESULTS: Turquoise and brown modules were found to be the most significantly related to tumorigenesis. Functional enrichment analysis showed that the turquoise module was associated with cell–cell adhesion, extracellular matrix and collagen catabolic process. A total of 10 hub genes (MMP1, TNFRSF12A, PLAU, FSCN1, PDPN, KRT78, EVPL, GGT6, SMIM5 and CYSRT1) were identified and validated at transcriptional and translational levels. Their genetic alteration and survival analysis were also revealed. CONCLUSION: We identified two modules and 10 hub genes, which were associated with the tumorigenesis of OSCC. The two modules provided references that will advance the understanding of mechanisms of tumorigenesis in OSCC. Moreover, the hub genes may serve as biomarkers and therapeutic targets for precise diagnosis and treatment of OSCC in the future.
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spelling pubmed-61579912018-10-01 Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis Zhang, Xiaoqi Feng, Hao Li, Ziyu Li, Dongfang Liu, Shanshan Huang, Haiyun Li, Minqi Onco Targets Ther Original Research PURPOSE: Oral squamous cell carcinoma (OSCC) is one of the most common malignant diseases worldwide, yet its molecular mechanisms are largely unknown. We aimed to construct gene co-expression networks to identify key modules and hub genes involved in the pathogenesis of OSCC. PATIENTS AND METHODS: We used dataset GSE30784 to construct co-expression networks by weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by Database for Annotation, Visualization and Integrated Discovery (DAVID). Hub genes were screened and validated by other datasets. RESULTS: Turquoise and brown modules were found to be the most significantly related to tumorigenesis. Functional enrichment analysis showed that the turquoise module was associated with cell–cell adhesion, extracellular matrix and collagen catabolic process. A total of 10 hub genes (MMP1, TNFRSF12A, PLAU, FSCN1, PDPN, KRT78, EVPL, GGT6, SMIM5 and CYSRT1) were identified and validated at transcriptional and translational levels. Their genetic alteration and survival analysis were also revealed. CONCLUSION: We identified two modules and 10 hub genes, which were associated with the tumorigenesis of OSCC. The two modules provided references that will advance the understanding of mechanisms of tumorigenesis in OSCC. Moreover, the hub genes may serve as biomarkers and therapeutic targets for precise diagnosis and treatment of OSCC in the future. Dove Medical Press 2018-09-19 /pmc/articles/PMC6157991/ /pubmed/30275705 http://dx.doi.org/10.2147/OTT.S171791 Text en © 2018 Zhang et al. This work is published and licensed by Dove Medical Press Limited The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License (http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed.
spellingShingle Original Research
Zhang, Xiaoqi
Feng, Hao
Li, Ziyu
Li, Dongfang
Liu, Shanshan
Huang, Haiyun
Li, Minqi
Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis
title Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis
title_full Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis
title_fullStr Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis
title_full_unstemmed Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis
title_short Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis
title_sort application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157991/
https://www.ncbi.nlm.nih.gov/pubmed/30275705
http://dx.doi.org/10.2147/OTT.S171791
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