Figure 4

Supervised cluster analysis for response to virus genes. Gene symbols for all Affymetrix probe sets were obtained by using the Bioconductor annotation package. Thereafter, all probe sets annotated to interrogate specific genes in the pathways of interest (response to virus) were retained, and agglomerative hierarchical clustering was performed by using the Ward method with 1-Pearson as the dissimilarity measure was applied to the pathway. Blue light boxes, normal liver tissues; black boxes, alcohol-cirrhotic liver tissues; pink boxes, HCV-cirrhotic liver tissues; green boxes, alcohol-HCV cirrhotic liver tissues.