As almost the totality of the identified DE lncRNAs in both conditions (Normal × Tumor and WT × BRAFV600E) is uncharacterized, we used prediction methods to identify a possible interaction between lncRNAs and mRNAs/microRNAs. Predicted mRNAs and microRNAs (targets of DE lncRNAs) were compared to differentially expressed mRNAs and microRNAs (log2 fold change >1 or <−1; adj. p-value < 0.05) calculated from the same TCGA patients. Predicted mRNAs/microRNAs that were also identified as DE were considered as indirectly validated targets.