Figure 1

Protein identification. (a) Protein identification from the cytoplasmic (purple), membrane (blue) and nuclear (pink) fractions of the Huh7 cells. Numbers of identified proteins with p ≥ 0.4 are shown. (b) Proteins identified in this study covered most of the 'biological process', 'cellular components' and 'molecular functions' categories at GO level 3. GO analysis was performed following the procedure described in [13]. Briefly, 16,477 human proteins currently carrying human GO nomenclatures were imported into the GoMiner program. Of the 16,477 human genes carrying GO annotations, 9,400 were loaded as Query Gene File in the GoMiner program to build a GO category structure based on the GO annotation database (June 2003). The 1,364 proteins were subsequently loaded as Query Changed Gene File in the GoMiner program to display coverage of the proteomics-identified proteins with respect to GO category. Of the 1,364 proteins, 815 that carry current GO annotations finally contributed to the coverage. (c) For immunoblot analysis, 20 μg of each lysate from IFN-treated Huh7 cells at the indicated time points and dose was subjected to western blot analysis using antibodies as indicated. Data at the 16 h time point and 400 IU/ml IFN concentration, which are the conditions for proteomic analysis, are highlighted with a blue box.