For downstream analyses, we increased the stringency of differentially expressed lncRNAs between Normal × Tumor (log2 fold change > 3 or < −3; adj. p-value <1 × 10−7, n = 73; Fig. 1D) and between WT × BRAFV600E (log2 fold change >2.5 or < −2.5; adj. p-value < 1 × 10−4, n = 59; Fig. 1E) to analyze the lncRNAs that were most DE. Hierarchical clustering was used to organize patients or lncRNAs into groups according to the expression levels of DE lncRNAs.