## 2 Results
### RNA Sequencing (RNA-seq) Analysis of Annotated Gene Transcripts  
The 5' capped RNA samples from HCV infected and control cells were analyzed by RNA sequencing and data processed as described in Experimental Procedures. Bioinformatics analysis of the data identified 100, 684, and 1844 differentially expressed annotated genes in acutely infected, as compared to mock infected, Huh 7.5 cells at 6, 48, and 72 hours, respectively (fold change \(\geq\) 1.50 and false discovery rate (FDR) \(>\) 13 (represents an untransformed FDR \(<\) 0.05 or 5 false positives out of 100) (Figure 1, Tables 1 and 2) [14]. \begin{table}
\begin{tabular}{|l|l|l|l|l|} \hline
**Ensembl Gene ID** & **Gene Name** & **Description** & **Fold Change** & **FDR** \\ \hline ENSG00000174951 & FUT1 & Fucosy/transferase 1 & 20.51 & 104.09 \\ \hline
**ENSG0000130487** & **KLHDTC7B** & **Kelch domain containing 7** & **18.93** & **141.94** \\ \hline
**ENSG0000136826** & **KLF4** & **Kruppel-like factor 4** & **15.10** & **142.63** \\ \hline ENSG0000128591 & FLNC & Filamin C & 13.38 & 1160.20 \\ \hline ENSG00000148677 & ANKRD1 & Ankyrin repeat domain 1 & 12.06 & 351.26 \\ \hline ENSG00000205595 & AREG & Amphiyeulin & 11.63 & 229.81 \\ \hline
**ENSG0000135842** & **Clor24** & **Chromosome 1 open reading frame 24 (Clorf24)** & **7.23** & **63.37** \\ \hline
**ENSG0000180535** & **MIST1** & **Xlass II bHLH protein MIST1** & **6.99** & **84.43** \\ \hline
**ENSG0000136383** & **ALPK3** & **Alpha-kinase 3** & **6.83** & **202.42** \\ \hline
**ENSG0000139269** & **INHE** & **Inhibin, beta E** & **6.40** & **1324.33** \\ \hline ENSG00000107731 & UNC5B & Unc-5 homolog B (C. elegans) & 6.17 & 265.31 \\ \hline ENSG0000049323 & LTBP1 & Latent transforming growth factor beta binding protein 1 & 6.14 & 129.49 \\ \hline
**ENSG0000048052** & **HDAC9** & **Histone deacetylase 9** & **6.09** & **137.83** \\ \hline
**ENSG0000198205** & **ZXDA** & **Zine finger, X-linked, duplicated A** & **6.02** & **47.22** \\ \hline
**ENSG0000111981** & **ULBP1** & **UL16 binding protein 1** & **6.01** & **37.66** \\ \hline
**ENSG0000130513** & GDF15 & Growth differentiation factor 15 & 5.90 & 958.30 \\ \hline
**ENSG0000122728** & **TAF1** & **TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor** & **5.54** & **41.06** \\ \hline
**ENSG0000138670** & **RASGF1B** & **RasGF domain family, member 1B** & 5.41 & **39.54** \\ \hline
**ENSG0000176971** & **LOC387758** & **Similar to RIKEN cDNA 111018M03** & **5.39** & **23.55** \\ \hline
**ENSG0000160999** & APS & **Adapter protein with pleckstrin homology and src homology 2 domains** & **5.18** & **22.09** \\ \hline \end{tabular}
\end{table} 
Table 1: The 50 most highly upregulated genes during acute HCV infection. The USeq DefinedRegionScanSeqs (DRSS) application was used to count the sequence reads for each annotated gene and score them for differential expression. The scores were controlled by multiple testing and ranked by transformed false discovery rate (FDR) and fold change (Experimental procedures). An FDR of 20 represents an untransformed FDR of 0.01 or 1 false positive per 100 observations and an FDR of 50 represents an untransformed FDR of 0.00001 or 1 false positive per 100,000 observations. Annotated genes that were significantly increased after acute HCV infection, relative to mock-infected cells, are presented in the order of their fold change. Newly identified differentially expressed genes are shown in bold. Genes marked with * had higher fold change at 48 h than at 72 h. A complete list of significantly upregulated genes is provided in Supplemental Table 1.