comb.p.adj.fdr	FDR adjusted combined p-value;
CpG	5′-cytosine-phosphate-guanine-3′
FDR	false discovery rate
GSEA	gene set enrichment analysis
HNSCC	head and neck squamous cell carcinoma
HPV	human papillomavirus
KEGG	Kyoto encyclopedia of genes and genomes
limma	linear models for microarray data
mean.mean.diff	value of the mean difference across all sites in a region
miRNA	micro ribonucleic acids
NA	not annotated; NTA, network topology-based analysis
OLL	oral lichenoid lesions
OLP	oral lichen planus
OPSCC	oropharyngeal squamous cell carcinoma
ORA	over-representation enrichment analysis
OSCC	oral squamous cell carcinoma
PCA	principal component analysis
PCR	polymerase chain reaction
RnBeads	integrated software package for the analysis and interpretation of DNA methylation data
SNPs	single nucleotide polymorphisms
TCGA	The Cancer Genome Atlas
TS	type-specific