To gain further insight into other pathways and genes that are regulated by Atg16l1, we generated transcriptional profiles of ileal tissue from wild-type mice and mice deficient in autophagy in epithelial cells (Atg16l1f/f x Villin-cre) or Cd11c+ cells (Atg16l1f/f x Cd11c-cre), after in vivo infection with Salmonella. Here, ITGAX is linked to infection.