!Name=ji-hepatology !ExptSetNo=1896 !Description=Interferon alfa (IFN-alpha) is an approved therapeutic agent for chronic hepatitis C. To directly characterize the effects of IFN-alpha in humans, we used microarrays to profile gene expression in peripheral blood mononuclear cells (PBMCs) from hepatitis C patients treated with IFN-alpha. Seven patients were studied using two strategies: (1) in vivo: PBMCs were collected immediately before the first dose of IFN-alpha, and 3 and 6 hours after the dose; (2) ex vivo: PBMCs that were collected before the first IFN-alpha dose were incubated with IFN-alpha for 3 and 6 hours. The microarray datasets were analyzed with significance analysis of microarrays (SAM) to identify genes regulated by IFN-alpha. We identified 516 named genes up-regulated at least 2-fold, at a false discovery rate (FDR) of less than 1%. In vivo and ex vivo studies generated similar results. No genes were identified as regulated differently between these 2 experimental conditions. The up-regulated genes belonged to a broad range of functional pathways and included multiple genes thought to be involved in the direct antiviral effect of IFN-alpha. Of particular interest, 88 genes directly relating to functions of immune cells were up-regulated, including genes involved in antigen processing and presentation, T-cell activation, lymphocyte trafficking, and effector functions, suggesting that IFN-alpha up-regulates multiple genes involving different aspects of immune responses to enhance immunity against hepatitis C virus. In conclusion, IFN-alpha-inducible genes can be identified in human PBMCs in vivo as well as ex vivo. Signature changes associated with different treatment outcomes may be found among these genes. !Name=jiI-Pa !Exptid=12392 !Name=jiI-Pm !Exptid=12606 !Name=jiI-P1-3 !Exptid=14292 !Name=jiI-P6-6(1) !Exptid=17461 !Name=WNR-P5IFNa6h !Exptid=17664 !Name=jiI-P3-9(2) !Exptid=17665 !Name=jiI-P4-3 !Exptid=17667 !Name=jiI-P6-6(2) !Exptid=17668 !Name=jiI-P3-9(1) !Exptid=17669 !Name=jiI-P3-3a !Exptid=17670 !Name=WNR-P3IFNa6h(2) !Exptid=17671 !Name=jiI-P3-3 !Exptid=17697 !Name=jiI-P3-9a(2) !Exptid=17700 !Name=jiI-P1-3a !Exptid=18407 !Name=jiI-P3-6 !Exptid=18408 !Name=jiI-P5-6(1) !Exptid=18420 !Name=jiI-P7-6(1) !Exptid=18650 !Name=WR-P7IFNa6h(2) !Exptid=18653 !Name=jiI-P6-3a(2) !Exptid=18772 !Name=WNR-P6IFNa6h(2) !Exptid=18773 !Name=jiI-P7-3 !Exptid=20995 !Name=jiI-P5-6(2) !Exptid=20996 !Name=jiI-P5-3a !Exptid=20998 !Name=jiI-P2-3 !Exptid=21000 !Name=jiI-P2-3a !Exptid=21003 !Name=jiI-P8-22 !Exptid=21010 !Name=jiI-P8-3a !Exptid=21290 !Name=jiI-P8-22a !Exptid=21291 !Name=jiI-P9-3 !Exptid=21383 !Name=jiI-P9-3a !Exptid=21384 !Name=jiI-P6-3 !Exptid=21962 !Name=jiI-P3-9a(1) !Exptid=24500 !Name=jiI-P4-22 !Exptid=24504 !Name=jiI-P5-3 !Exptid=24537 !Name=jiI-P8-3 !Exptid=24538 !Name=jiI-P6-3a(1) !Exptid=24540 !Name=WNR-P3IFNa6h(1) !Exptid=25353 !Name=WNR-P6IFNa6h(1) !Exptid=25357 !Name=WR-P7IFNa6h(1) !Exptid=25358 !Name=jiI-P5-6(3) !Exptid=25377 !Name=jiI-P6-6(3) !Exptid=25380 !Name=jiI-P7-6(2) !Exptid=25381 !Name=jiI-P10-3 !Exptid=26704 !Name=jiI-P10-6 !Exptid=26705 !Name=jiI-P10-3a !Exptid=26706 !Name=WR-P10IFNa6h(2) !Exptid=26707