Additional file 1: Table S1. Gene ontology and KEGG pathway analysis of DEGs associated with aberrant miRNA between early stage and late stage samples. Table S2. Gene ontology and KEGG pathway analysis of DEGs associated with aberrant DNA methylation between early stage and late stage samples. Table S3. DEGs associated with both specific miRNA and DNA methylation CpG sites between early and late stage. Figure S1. Transcription factors predicted for hub genes HNRNPA1,PPIF and MCL1 (2 transcription factors per gene.