Genes differentially expressed in congenic mice compared to healthy controls. Panels a to f show gene graphs of genes differentially expressed with false discovery rate of 0.0: (a) B10.Q versus NB, 'standard analysis' (71 genes); (b) B10.Q versus NB, 'alternative analysis' (8 genes); (c) B10.Q versus NBI, 'standard analysis' (271 genes); (d) B10.Q versus NBI, 'alternative analysis' (61 genes); (e) NB versus NBI, 'standard analysis' (59 genes); and (f) NB versus NBI, 'alternative analysis' (19 genes). Upregulated and downregulated genes in the congenic mice are presented by red and green lines, respectively. The genes within the nonobese diabetic (NOD) congenic fragments on the lists of differentially expressed genes were selected and clustered by K-means clustering to identify co-regulation of genes within the fragments. Also presented are differentially expressed genes in fragments Idd5 (blue) and Nss1 (black) for the (g) B10.Q versus NB and (h) B10.Q versus NBI comparisons. The gene expression values are log2 transformed and mean normalized. The abscissa indicates the individual mice and the ordinate shows the gene expression intensities. The congenic mice are denoted NB (B10.Q.Nss1) and NBI (B10.Q.Nss1/Idd5-he and B10.Q.Nss1/Idd5-ho).