This study performed a differential transcriptomic and metabolomic analysis of benign proliferative and transformed liver. They used partial hepatectomy-induced liver regeneration and diethylnitrosamine (DEN) induced carcinogenesis to identify and analyze alterations specific to multiple regenerative and transformed tissue states. This dataset contains supplementary data tied to the publication. The supplementary data includes tables, which contains RNAseq data for quiescent and regeneration tumor samples, RNAseq data for quiescent and sham samples, relative abundance of metabolites from quiescent and regeneration tumor tissue samples, relative abundance of metabolites from quiescent and regeneration plasma samples, concentration of lipid metabolites from quiescent and regeneration tissue samples, concentration of lipid metabolites from quiescent and regeneration plasma samples, order of metabolites and genes in heat maps, genotype of tumors analyzed for common oncogenes, and data for volcano plot.