We therefore propose that multiple IBD genes play an important role within the intestinal epithelium in terms of transcriptional regulation of the type I interferon response to viral pathogens (SBNO2, NFKB1, IFIH1, ZFP36L1, IRF1, GIGYF1, OTUD3, and AIRE) and others in the transcriptional regulation of the anti-bacterial response (NFKB1, NOD2, and PITX1). Here, AIRE is linked to inflammatory bowel disease.