Pathways over-represented in the lists of differentially expressed genes. (a) 'Interferon gamma signalling pathway' in the B10.Q versus B10.Q.Nss1 gene list; (b) 'Toll-like receptor signalling pathway'; and (c) 'Inflammation mediated by chemokine and cytokine signalling pathway' in the B10.Q versus B10.Q.Nss1/Idd5 gene list. The coloured boxes represent the genes present in our gene list, and the colours indicate fold change (FC), where positive FC indicates upregulation in the congenic mice. Red and blue genes have FC above 2 and FC below -2, respectively. Orange and green have FC from 1.5 to 2 and -2 to -1.5, respectively. Yellow and light blue are upregulated and downregulated, respectively, with FC < 1.5.