Fully understanding the underlying variance between HLCs and whole livers merits further investigation, as hepatocytes constitute only one of several cell types in the liver. We quantified differential gene expression using DESeq2 (Love et al., 2014). We identified 3,709 genes more highly expressed in livers compared to iPSCs and 2,040 genes more highly expressed in HLCs compared to iPSCs at FDR < 5%. We sought to assess the liver-specific functions associated with 1,349 genes that were common to both sets (differentially expressed in both HLCs and livers compared to iPSCs) by estimating the enrichment of these genes for gene ontology (GO) terms. We identified 126 common GO terms including functions specific to hepatic regulation and lipid metabolism (Table S2).
