Identification of DEGs in oral cancer between HPV-negative and HPV-positive patients
To determine the effects of HPV on oral cancer, we analyzed the RNA-seq data from the HPV-negative and -positive oral squamous cell carcinoma Patients. A total of 575 genes were identified with the threshold of P < 0.01. The top up- and down-regulated genes were indicated by the heatmap and volcano plot (Figure 1). The top ten DEGs were listed in Table 1.
Enrichment analysis of DEGs between HPV-negative and HPV-positive patients
To further understand the potential biological processes, we performed the KEGG and GO analyses (Figure 2). The significant KEGG items includes “PI3K−Akt signaling pathway”, “Human papillomavirus infection”, “Focal adhesion”, “ECM−receptor interaction”, “Small cell lung cancer”, “Amoebiasis”, and “Arrhythmogenic right ventricular cardiomyopathy”. We identified the BP of GO including “Extracellular matrix organization”, “Extracellular structure organization”, “External encapsulating structure organization”, “Connective tissue development”, “Collagen metabolic process”, “Collagen fibril organization”, “Endodermal cell differentiation”, “Endoderm formation”, “Basement membrane organization”, and “Protein hydroxylation”. We identified the CC of GO including “Collagen−containing extracellular matrix”, “Endoplasmic reticulum lumen”, “Focal adhesion”, “cell−substrate junction”, “basement membrane”, “collagen trimer”, “lysosomal lumen”, “complex of collagen trimers”, “microfibril”, and “fibrillar collagen trimer”. We then identified the MF of GO including “extracellular matrix structural constituent”, “growth factor binding”, “collagen binding”, “metalloendopeptidase activity”, “integrin binding”, “iron ion binding”, “extracellular matrix structural constituent conferring tensile strength”, “extracellular matrix binding”, “L−ascorbic acid binding”, and “platelet−derived growth factor binding”.
PPI network analysis
To determine the potential relationship among the DEGs, we constructed the PPI network by using 509 nodes and 1417 edges. We set the combined score > 0.2 as a cutoff by using the Cytoscope software. Table 2 showed the top ten genes with the highest scores. The top two significant modules were indicated in Figure 3. We further analyzed the PPI and DEGs with Reactome map (Figure 4) and identified the top ten functional processes including "Extracellular matrix organization", "Collagen formation", "Assembly of collagen fibrils and other multimeric structures", "Collagen biosynthesis and modifying enzymes", "ECM proteoglycans", "Non-integrin membrane-ECM interactions", "Post-translational protein phosphorylation", "Degradation of the extracellular matrix", "Elastic fibre formation", and "Laminin interactions" (Supplemental Table S1).