In the present study, we reported a comprehensive characterization of ncRNA expression profiles in HCC, a novel MEG3 isoform with potential oncogenic function in vitro, and the construction of a MEG3-predominated MLMI network using significantly DE lncRNAs, miRNAs and mRNA to reveal multiple interactions among these molecules during post-transcriptional regulatory processing. Here, MEG3 is linked to hepatocellular carcinoma.