Differential expression of IRF1 in HCV cirrhotic as compared to control liver.
Panel A. Expression of IRF1 as measured by signal intensity on ENCODE tiling arrays is displayed using the Integrated Genome Browser (IGB). The y-axis represents the log2 transformation of the normalized signal divided by the background signal on arrays and each bar represents the normalized signal intensity of probes hybridized to 60mer targets tiled across the gene region (Methods). Genomic regions that are tiled yet lack a signal are indicated by a baseline tick mark. Absence of a tick mark indicates no probes in that region. Gene structure, orientation, and chromosomal location are shown in black. Average RNA expression based on the analysis of 5′ capped RNA isolated from HCV cirrhotic and control liver is depicted in green for both HCV cirrhotic and control liver. Average RNA expression using poly(A)+ RNA is depicted in blue. Differences in expression between HCV cirrhotic and control liver for poly(A)+ and 5′ capped RNA populations are depicted as window level false discovery rates in red (-10Log10 FDR) (see Methods). A transformed FDR of ≥13 (represents an untransformed FDR ≤0.05 or 5 false positives out of 100) was considered statistically significant. PanelB. qPCR was performed as described in Methods. Triplicate samples from seven HCV cirrhotic, seven mild HCV (no fibrosis), and ten control livers were analyzed. HCV Cirrhotic 1 and Control 1 refer to the original samples used for the ENCODE tiling array analysis. The mean ± SEM fold change for each specimen analyzed is shown and the location of the qPCR primers is indicated by qPCR in Panel A. P-values were calculated using the Student's t-test.