The LCL gene expression response to IFN-β.

<p>A: Volcano plot for the IFN-β gene expression response in LCLs. Log2(fold change) of expression levels following IFN-β exposure and P-values (one-way ANOVA) are depicted for each transcript probe. The horizontal dashed line represents the threshold for the adjusted P-value of 0.05. Vertical dashed line indicates threshold of log2(fold change)>1 and <−1. Differentially expressed genes (in black) are genes with log2(fold change) ≥1 and adjusted P-value ≤0.05, novel IFN-β response genes included in RTPCR validation analyses are marked. For pathways analyses a lower threshold was employed (dotted vertical line) with log2(fold change)≥0.4 (dark grey dots). B: Venn diagram describing the proportion of differentially expressed genes in response to IFN-β [log2(fold change)≥1, adjusted P-value<0.05, bold outlined ellipse] that are novel response genes (grey shade), and a comparison to the published differentially expressed genes up-regulated in LCLs in comparison to primary B cells, based on the data of Caliskan and colleagues [log2(fold change)≥1, adjusted P-value<0.05]<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102331#pone.0102331-Caliskan1" target="_blank">[26]</a>. Definition of novel IFN-β response genes is based on the Interferome V2.01 database (accessed 19.8.13) search for the 115 IFN-β response differentially expressed genes. Numbers indicate the number of genes within each subgroup.