Supplementary material for this article can be found on the H EPATOLOGY Web site ( ).

jws-hep.21751.tbl1.xls1018KSupplementary Table 1. Comprehensive list of the 5,920 identified liver proteins resulting from proteomic analysis of the Huh-7.5 HCV replicon system and, normal and cirrhotic (HCV- and HCV+) human liver tissue. Included is the number of different peptides and total peptide identifications for each protein detected in each sample source.
jws-hep.21751.tbl2.xls1326KSupplementary Table 2. Comprehensive list of all liver biopsy proteins quantified in this study. Final protein abundance ratios and accompanying P-values were calculated in Elucidator by combining data from technical replicates. Also reported here are the log protein abundance ratio, log error, and X Dev (log ratio/log error). For samples 195 and 203 only two technical replicates were used to calculate the final protein abundance ratios. This resulted from an outlier replicate for sample 195 (e.g. correlation coefficient of < 0.5 when compared to the other 2 technical replicates) and an aberrant LC-MS run (most likely a sample loading error) for sample 203. All other samples reflect the results obtained from combining data from 3 technical replicates.
jws-hep.21751.tbl3.xls354KSupplementary Table 3. Comprehensive list of proteins exhibiting statistically significant differences among fibrosis groups. The 210 proteins exhibiting statistically significant (P < 0.05) differences between fibrotic groups (e.g. stages 0-4) and used to generate the cluster shown in Figure 5 are reported here. Included are the protein abundance ratios and accompanying P-values as well as the log protein abundance ratio, log error, fold-change, X Dev (log ratio/log error), and hierarchical clustering order.

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