In the gene-metabolic networks that were constructed with genes and metabolites specifically deregulated in different NAFLD phenotypes, we identified the dysfunction of lipid and fatty acid metabolism and PPAR signaling pathway in HFD rats; the dysfunction of immune and inflammatory response, programmed cell death, and NF-κB signaling pathway in MCDD rats; and the dysfunction of glycosyl compound biosynthetic process, response to insulin and AMPK signaling pathway in HFD+STZ rats (Figure 5). Here, PPARA is linked to metabolic dysfunction-associated steatotic liver disease.