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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.