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Updated: Apr 19, 2026
Development of Compendium for Esophageal Squamous Cell Carcinoma
Published on: April 12, 2024
Comprehensive network analysis of genes expressed in human oropharyngeal cancer
Yang Yu1, Simin Li1, Han Wang2
1Department of Periodontology, The Stomatology Affiliated Hospital of Harbin Medical University, 143 Yiman Street, Nangang District, Harbin, Heilongjiang, China.
Purpose:
Oropharyngeal cancer (OPC) is the eighth most common cancer worldwide, however the genes involved in the development of OPC have been reported few. We constructed a co-expression network to extend knowledge of the molecular biomarkers in OPC development.
Materials And Methods:
Microarray data of HPV-active, -inactive, -negative OPC and normal benign tissue (uvula, tonsil) (Series GSE55550) were retrieved from NCBI GEO DataSets. We performed co-expression analysis of OPC transcriptome data by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off using 13 guide genes.
Results:
The OPC subnetwork contained three clusters: cell cycle (62 node genes and 125 edge genes), immune system (44 node genes and 70 edge genes) and organ morphogenesis (128 node gene and 215 edge genes) process separately.
Conclusion:
Our co-expression analysis includes separated transcriptomes of OPC, which is a useful resource for OPC researchers to elucidate important and complex biological events, to prevent and to predict cancer.
Insights
This study built a gene co-expression network to identify molecular biomarkers for oropharyngeal cancer (OPC). The network revealed key genes involved in cell cycle, immune system, and organ morphogenesis, aiding OPC research.
Area of Science:
- Oncology
- Genomics
- Bioinformatics
Background:
- Oropharyngeal cancer (OPC) is a significant global health concern, ranking as the eighth most common cancer worldwide.
- Limited knowledge exists regarding the specific genes driving OPC development, necessitating further molecular investigation.
Purpose of the Study:
- To construct a gene co-expression network to expand understanding of molecular biomarkers in OPC.
- To identify key biological processes and genes implicated in OPC pathogenesis.
Main Methods:
- Utilized microarray data from NCBI GEO DataSets (Series GSE55550) for HPV-active, -inactive, and -negative OPC, alongside normal tissues.
- Performed co-expression analysis using the Pearson correlation coefficient (PCC) with a mutual rank (MR)-based cutoff and 13 guide genes.
Main Results:
- Identified three distinct clusters within the OPC co-expression subnetwork: cell cycle (62 nodes, 125 edges), immune system (44 nodes, 70 edges), and organ morphogenesis (128 nodes, 215 edges).
- These clusters highlight critical biological processes influenced by specific gene sets in OPC development.
Conclusions:
- The developed co-expression network provides a valuable resource for OPC researchers.
- Facilitates deeper elucidation of complex biological events, contributing to improved prevention and prediction strategies for oropharyngeal cancer.
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