HCC tissue vs. Non-tumor liver tissue

The expression ratio between the experimental and reference samples (Cy5/Cy3 ratio) was determined using ImaGene 5.2 (BioDiscovery). The correlation between the intensity value for each cDNA from the hepatocellular carcinoma (HCC) and reference tissues was examined using scatter plots, and a linear relationship was obtained in log space. All spots with signal intensities <50% of those of the local background were eliminated. The data were normalized using the print tip loess normalization with the limma in R packages on Bioconductor. Genes with expression values >80% of the entire tissues were retained for further analysis. A hierarchical clustering algorithm was used in all tissues and genes using the Pearson uncentered correlation coefficient as a similarity measure and complete linkage clustering in TIGR MultiExperiment Viewer (version 3.11) software. A two-sample t test based on 10,000 random permutations in the R packages was used to statistically analyze the differentially expressed genes.