2. Differential gene expression in whole blood from SJIA patients and healthy controls. A. Data were normalized in Beadstudio using the "average" method and imported into Genespring 7.3 (Agilent) where the expression value for each gene was normalized to the median expression value of that gene’s measurement in the healthy controls. To identify transcripts differentially expressed between study groups that might serve as classifiers, class comparison analyses were performed on probe sets that were considered “present” (p<0.01) and had a signal greater than 50 in at least 75% of samples in each group (QC probe). Non parametric testing (Wilcoxon-Mann-Whitney U-test; p<0.01 for class comparisons with Benjamini correction; p<0.05 for modular analyses with no multiple testing corrections) was used to rank genes based on their ability to discriminate among pre-specified groups of patients. 9,477 genes passing the control criteria were tested. Genes expressed at statistically different levels between the 2 groups (p<0.001, Wilcoxon-Mann-Whitney test, Benjamini correction) were rearranged by hierarchical clustering in order to reveal differential expression. A list of the genes shown in this figure is available in Supplementary Table S2. B. The above gene list was analyzed using Ingenuity Pathways. The most significant identified network is represented.