Differentially Expressed Genes Associated with Immune Response.

Pol II RNA transcripts were isolated from HCV cirrhotic and control liver
via two methods. 5′ capped RNA was isolated using a high affinity
variant eIF4E protein, poly(A)+ RNA was isolated with oligo-dT
(Qiagen) and cDNA was synthesized with random primers (Methods). RNA
transcript expression was measured by averaging fluorescent signal
intensity on Agilent's ENCODE gene arrays for each sample
(Methods). Differences in gene expression were visualized using
Genoviz's Integrated Genome Browser software. Only annotated genes
with ≥1.5 fold and Bonferroni corrected p values <0.05 between HCV
cirrhotic and control liver are listed with details of their expression.
Genes are listed by the specific pool of RNA analyzed. No genes with
decreased expression in HCV cirrhotic liver were found in the
poly(A)+ RNA. Genes which have been previously documented to have
increased expression in HCV cirrhotic liver are marked with *. Only
genes associated with the immune response are listed above. A complete
list of differentially expressed genes is provided in supplemental
materials.