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This article is part of the supplement: Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Genomics

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Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma

Lin Wei12, Baofeng Lian34, Yuannv Zhang2, Wei Li3, Jianren Gu2, Xianghuo He2* and Lu Xie3*

Author Affiliations

1 Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China

2 State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P. R. China

3 Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, P. R. China

4 School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China

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BMC Genomics 2014, 15(Suppl 1):S13  doi:10.1186/1471-2164-15-S1-S13

Published: 24 January 2014



Hepatocellular carcinoma (HCC) is one of the most highly malignant and lethal cancers of the world. Its pathogenesis has been reported to be multi-factorial, and the molecular carcinogenesis of HCC can not be attributed to just a few individual genes. Based on the microRNA and mRNA expression profiling of normal liver tissues, pericancerous hepatocellular tissues and hepatocellular carcinoma tissues, we attempted to find prognosis related gene sets for HCC patients.


We identified differentially expressed genes (DEG) from three comparisons: Cancer/Normal, Cancer/Pericancerous and Pericancerous/Normal. GSEA (gene set enrichment analysis) were performed. Based on the enriched gene sets of GO terms, pathways and transcription factor targets, it was found that the genome instability and cell proliferation increased while the metabolism and differentiation decreased in HCC tissues. The expression profile of DEGs in each enriched gene set was used to correlate to the postoperative survival time of HCC patients. Nine gene sets were found to prognostic correlation. Furthermore, after substituting DEG-targeting-microRNA for DEG members of each gene set, two gene sets with the microRNA expression profiles were obtained that had prognostic potential.


The malignancy of HCC could be represented by gene sets, and pericancerous liver exhibits important characteristics of liver cancer. The expression level of gene sets not only in HCC but also in the pericancerous liver showed potential for prognosis implying an option for HCC prognosis at an early stage. Additionally, the gene-targeting-microRNA expression profiles also showed prognostic potential, demonstrating that the multi-factorial molecular pathogenesis of HCC is contributed by various genes and microRNAs.

Hepatocellular Carcinoma; Gene Expression Profile; Gene Set Enrichment Analysis; Prognosis; microRNA