Logistic regression modeling of patient data.

<p>*OR for gene expression is for a change of 10 units.</p

IL28 Genotype analysis (112/130 patients).

<p>IL28 Genotype analysis (112/130 patients).</p

Patient Demographics.

<p>Patient Demographics.</p

Expression of the IFN Gene Signature.

<p><b>Key:</b>^a,ISRE-driven ISGs, ^b ISRE-driven ISGs potentially regulated by NF-κB, ^c SIE-driven ISGs, and ^d SIE-driven ISGs potentially regulated by NF-κB.</p

Genes in IRF activation by cytosolic pattern recognition receptors are associated with IFN responsiveness.

<p>The gene network was generated using Ingenuity Pathway Analysis software. Genes upregulated in nonresponders (shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104202#pone-0104202-g001" target="_blank">Figure 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104202#pone-0104202-g002" target="_blank">2</a>) were highlighted.</p

Differential expression of an IFN-regulated signature geneset in relapsers versus responders to IFN-ribavirin therapy to therapy.

<p>Expression of an IFN signature geneset was determined in RNA extracted from FFPE liver biopsies by nCounter analysis. Boxplots of genes found to be statistically differentially expressed by nonparametric Mann-Whitney analysis (p<0.05).</p

Genes in the pattern recognition receptor pathway are associated with IFN responsiveness.

<p>The gene network was generated using Ingenuity Pathway Analysis software. Genes upregulated in nonresponders (shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104202#pone-0104202-g001" target="_blank">Figure 1</a>) were highlighted. As expected, several antiviral signaling pathways were overrepresented in these genes.</p

Differential expression of an IFN-regulated signature geneset in responders versus nonresponders to therapy.

<p>Expression of an IFN-regulated signature geneset was determined in RNA extracted from FFPE liver biopsies by nCounter analysis. Boxplots of genes found to be statistically differentially expressed by nonparametric Mann-Whitney analysis (p<0.05).</p

Signaling networks of genes that are associated with IFN responsiveness.

<p>The gene network was generated using Ingenuity Pathway Analysis software.</p

The distribution of predicted probability of therapeutic response (with relapsers included).

<p>We found that those who actually responded to IFN-ribavirin treatment had higher predicted probabilities of response in the model.</p