We performed a similar set of analyses on surgical material and core biopsy specimens obtained from HCV-infected patients with liver cirrhosis [11] . Importantly, this study also included an analysis of normal liver samples to determine normal physiologic variation in gene expression. To identify markers associated with cirrhosis, genes that were differentially expressed in normal liver, or in HCC, were subtracted from the set of genes differentially expressed in cirrhotic livers. The resulting gene set included genes expressed in activated lymphocytes infiltrating the cirrhotic liver and genes involved in the remodeling of the extracellular matrix, cell-cell interactions associated with cytoskeleton rearrangements, the anti-apoptotic pathway of Bcl-2 signaling, and the interferon response. Together, this analysis identified several potential gene expression markers of HCV-associated liver disease and contributed to our rapidly expanding database of experiments describing HCV pathogenesis.