Among these dysregulated RNAs, three DELs (AP002478.1, HTR2A-AS1, and ERVMER61-1) and six DEGs (enhancer of zeste homolog 2 [<i>EZH2</i>], kinesin family member 23 [<i>KIF23</i>], chromobox 2 [<i>CBX2</i>], centrosomal protein 55 [<i>CEP55</i>], cell division cycle 25A [<i>CDC25A</i>], and claspin [<i>CLSPN</i>]) were used for construct a prognostic signature for HCC overall survival (OS), and performed well in HCC OS (adjusted <i>P</i><0.0001, adjusted hazard ratio = 2.761, 95% confidence interval = 1.838-4.147).