Copper is an essential trace element, however, at supraphysiological levels it can be extremely toxic. Microarray data from HepG2 cells exposed to 100, 200, 400 and 600 µM copper for 4, 8, 12 and 24 h were generated and analyzed. Principal components, K-means and hierarchical clustering, interactome, and pathway mapping analyses indicate that these exposure conditions induce physiological and toxicological changes in the HepG2 transcriptome. As a general trend; when the level of toxicity increases, the number and diversity of affected genes, Gene Ontology categories, regulatory pathways, and complexity of interactomes increase. Physiological responses to copper include transition metal ion binding and response to stress/stimulus; while toxicological responses include apoptosis, morphogenesis and negative regulation of biomolecule metabolism. The global gene expression profile was overlaid onto biomolecular interaction networks, and signal transduction cascades using pathway mapping and interactome identification. This analysis indicates that copper modulates signal transduction pathways associated with MAPK, NF-B, death receptor, IGF-1, hypoxia, IL-10, IL-2, IL-6, EGF, Toll-like receptor, protein ubiquitination, xenobiotic metabolism, leukocyte extravasation, complement and coagulation, and Sonic Hedgehog signaling. These results provide insights into the global and molecular mechanisms regulating the physiological and toxicological responses to metal exposure.