Pathways representing a set of autoimmune diseases (i.e., viral myocarditis, type I diabetes mellitus, systemic lupus erythematosus, autoimmune thyroid disease, allograph rejection, graph-versus-host-disease, asthma, leishmaniasis and prion diseases) and disease-associated immune signatures (i.e., antigen processing and presentation, intestinal immune network for IgA production and complement and coagulation cascades) were activated with MHC class II autoantigens as common lead genes (Fig. 3D, Additional file 12: Fig. S3D). This evidence concerns the gene CD79A and autoimmune thyroid disease.