Fig. 1

Differentially expressed genes between tumors and adjacent non tumor tissues. a Demographic and clinicopathological data of the 25 HCC patients recruited in this study. HCC staging was classified according to tumor-node-metastasis system by the American Joint Committee on Cancer. b Differentially expressed genes between tumor and adjacent non-tumor tissues. Top: The number of differentially expressed transcripts/genes at various stages of the workflow. Bottom: Heat-map of the 4462 differentially expressed genes in tumors and adjacent non-tumor patient samples. c Significant pathways associated with the differentially expressed genes between tumors and adjacent non-tumors. FDR < 0.01. Z-score predicts the activation status of the pathway. FDR denotes False Discovery Rate. d Characteristics of upstream regulators. e Network of genes associated with the most activated regulatory molecule, TP73. f Differentially expressed genes associated with clinical parameters. I–III The genes associated with clinical parameters. The X-axis represents the fold-change of gene expression between tumors and adjacent non-tumorous tissues (T/N). The Y-axis represents the fold-change of gene expression between patients with less favorable clinical outcome (i.e. higher grade (poor), greater vascular invasion (VI+) and poorer survival) versus those with more favorable clinical outcome (i.e. lower grade (good), less vascular invasion (VI−) and better survival). The size of the bubble represents the − log-₂ (FDR) of gene expression between T and NT. HR denotes hazard ratio. (IV) Biological pathways associated with differentially expressed genes associated with the various clinical characteristics. The X-axis shows the pathways that are significantly associated with clinically associated genes for the different clinical phenotype. A red bar shows genes which are upregulated in tumors relative to the non-tumors associated with a worse clinical outcome, while a green bar represents genes downregulated in tumors relative to the non-tumors associated with a worse clinical phenotype