Fig. 4

Gene profiling analysis of four types of sample including high SKA1, low SKA1, fetal liver and hepatocytes (adult liver) based on microarray data. The dendrogram and heatmap (a) show the hierarchical cluster analysis of gene-expression data from human specimens of hepatocytes, fetal liver and HCC tissues. Columns represent individual samples, and rows represent individual genes. Each cell in the matrix represents the expression level of a gene in an individual sample. The scale bar indicates the level of expression, red indicates a high level of expression, and green a low level of expression. GSEA analysis showed that genes upregulated in high SKA1 HCC enriched in the cell cycle pathway (b), while genes down-regulated in the high SKA1 HCC were enriched in the apoptosis pathway (c). NES denotes normalized enrichment score in gene set enrichment analysis. The ranked list metric was generated by calculating the signal-to-noise ratio which is based on the difference of means scaled according to the standard deviation. The larger the signal-to-noise ratio, the more distinct the gene expression is in each phenotype and the more the gene acts as a “class marker.” The bar codes stand for genes in the pathway. The Broad Institute Gene Set Enrichment Analysis website (http://software.broadinstitute.org/gsea/index.jsp) provides detailed information about the computational method