The three most frequent patterns of miRNA responses were (i) a TLR-specific response (N = 65, 19% of DE miRNAs), as in the case of the NF-κB inhibitors miR-9-5p (Fig. 3d) and miR-155-5p; (ii) a viral-stimuli specific response (R848 and IAV, N = 55, 16% of DE miRNAs), such as miR-3614-5p recently involved in Crohn’s disease susceptibility [50] (Fig. 3e); and (iii) an IAV-specific response (N = 78, 23% of DE miRNAs), as attested by the pro-inflammatory mir-429 or the TRIM22 repressor mir-215-5p (Fig. 3f). Here, NFKB1 is linked to Crohn disease.