Fig. 2

lncRNA clusters and other molecular aberrations. a LncRNA-based clustering of HNSCC samples is significantly associated with clustering based on diverse molecular features, mainly DNA methylation and expression of PCGs (mRNA). Significance values are plot upon chi-square test computation. b, c Association with HPV infection and HNSCC mutations with lncRNA clusters. Chi-square or odds ratio values are plot upon chi-square test (b) or Fisher’s exact test (c) computation, respectively. Dashed red line: threshold of significance (p val <0.05). d Distribution of lncRNA clusters and HPV-infected samples or samples with mutations in KMT2D or NSD1. Note the enrichment of HPV infection in c5, the NSD1 mutations in c1, and the KMT2D mutations in c2 (red lines) and the depletion of KMT2D mutations in c4 (green line). p values are calculated with Fisher’s exact test. Vertical black lines in d showed HPV+ samples and mutated samples for the selected genes KMT2D and NSD1, respectively