This analysis showed that C1 (T1D and CD) was characterized by the enrichment of pathways associated with lymphocyte differentiation and activation (i.e., MHC assembly), C2 (SLE, RA, AIT) was associated with the regulation of the ERK1/2 cascade (plays an essential role downstream of immune receptors to elicit inflammatory gene expression in response to infection and cell or tissue damage), while C3 (Crohn’s disease and Colitis) had a response to bacterium and metal ion transport. This evidence concerns the gene HLA-C and Crohn disease.