In NEC tissues, we identified target miRNAs which could potentially act on the key receptor TLR4, transcription factors NFκB/NFKB2, AP-1/FOXA1, HIF1A and downstream effector genes in functional networks of angiogenesis, arginine metabolism, cell adhesion/chemotaxis, ECM remodeling, hypoxia/oxidative stress inflammation and muscle contraction, whereas dysregulated miRNAs in SIP tissues were mainly directed towards mRNAs associated with G-protein mediated muscle contraction. Here, FOXA1 is linked to necrotizing enterocolitis.