Differential expression analyses were also performed to identify BRAFV600E-correlated lncRNAs. The comparison between BRAF wild type (WT) patients (n = 242) and BRAFV600E patients (n = 226), determined 437 differentially expressed lncRNAs (log2 fold change > 1 or < −1; adj. p-value 1X10−4; Fig. 1B), being 117 upregulated and 320 downregulated (Supplemental Table S4). The same comparison found a total of 924 mRNAs (log2 fold change > 1 or < −1; adj. p-value < 0.05; Supplemental Table S5) and 94 microRNAs (log2 fold change > 1 or < −1; adj. p-value < 0.05; Supplemental Table S6) differentially expressed. A total of 103 lncRNAs was differentially expressed in both analyses [(Normal × Tumor and WT × BRAFV600E), (Fig. 1C, Table 1 and Supplemental Table S7)].Table 1Top 5 upregulated and 5 downregulated common DE lncRNAs between Normal × Tumor and WT × BRAFV600E.Ensembllog2 FCAdj. p-valuelog2 FCAdj. p-valueN × TN × TWT × BRAFV600E WT × BRAFV600E ENSG00000214797.3 7.016.39E-095.194.92E-12 ENSG00000273132.1 5.494.17E-101.693.70E-12 ENSG00000230918.1 5.491.17E-101.363.89E-05 ENSG00000260328.1 5.394.27E-084.042.26E-16 ENSG00000256268.1 5.122.27E-141.004.52E-13 ENSG00000261185.1 −6.421.13E-10−2.813.55E-06 ENSG00000254489.1 −6.377.98E-15−3.278.33E-11 ENSG00000260412.1 −6.337.11E-09−3.772.59E-08 ENSG00000235070.3 −4.972.28E-12−3.011.10E-15 ENSG00000247416.2 −4.556.89E-13−2.401.09E-16