We have identified 455 DE lncRNAs between paired normal and PTC samples. A total of 76 (log2 fold change >1 or < −1; adj. p-value < 1 × 10−7) lncRNA were previously reported as DE in thyroid cancer compared to adjacent normal thyroid36 (Fig. 5A and Supplemental Table S12). This validation set, together with the lncRNAs confirmed by experimental approaches (Fig. 2 and Supplemental Fig. S1), confers consistency to our analysis. Additionally, a diversity of DE lncRNAs identified in our analysis were reported in individual studies as altered in PTC samples, such as ENSG00000259104.2 38, 39, ENSG00000236130 40, ENSG00000226363 37, ENSG00000271086 39, 41, ENSG00000223914 37 and ENSG00000187979 37.Figure 5Experimentally validated lncRNAs are important to tumor malignancy. (A) Examples of DE lncRNAs between Normal and PTC, which were confirmed in a validation set36. (B) Differentially expressed lncRNAs in PTC that alter tumor malignancy.