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To explore the underlying biological mechanisms of different biocompatibility between bare and TiN-coated NiTi alloys, gene expression profiles of which were compared using microarray methods. The gene expression profiles of human umbilical vein endothelial cells (HUVECs) were analyzed after the cells were cultured on bare and TiN-coated NiTi alloys for 24, 48 and 72 h, respectively. We revealed that 21.4% genes (8772 out of 41000) displayed differential expression upon treatment with TiN-coated alloys, compared to 15.2% genes (6253 out of 41000) with uncoated alloys. Our results indicate that the TiN-coated and uncoated NiTi alloys in human cells are capable of eliciting different cellular responses at the molecular level.