Background: Gadolinium endohedral metallofullerenol [Gd@C82(OH)22]n is a new potential nanoparticle, which is developed by Chinese Academy of Sciences, for the cancer treatment.However, the mechanism of this anti-cancer nanoparticle remains mostly unknown.A good understanding of the regulation and pathways that inhibit the growth of tumor cells can provide guidance to the design of new cancer treatment.Methods: In order to elucidate the anti-cancer mechanism of [Gd@C82(OH)22]n, we measure the gene expression profiles of the human breast cancer cells (MCF-7) and the human umbilical vein endothelial cells (ECV304.) treated with and without [Gd@C82(OH)22] n respectively using the Agilent Gene Chip G4 112F.The treated and untreated samples of the ECV304 cells are hybridized to one chip and those of MCF-7 cells are hybridized to another.We analyze data as follows.First, we normalize the two chips independently using the subsub normalization method.This is the first time we report the results of sub-sub normalization to the Agilent Gene Chip.Second, we use Wilcox test to infer the up-regulation or downregulation pathways and GO sets.Third, we infer several transcription factors (TFs) using BASE method.Results: The results from the above normalization and summarization methods are more reasonable than the results from the method used by Agilent Corporation.Based on the data, we could provide several hypotheses regarding the mechanism of this nanoparticle, some of which are consistent with earlier experimental results.Conclusions: Functional genomics is a powerful tool to discover the molecular mechanism of [Gd@C82(OH)22]n.We obtained some insights including the cells growth and the immune response, which are validated by the papers published by Nanomaterials and Nan0safety National Center.We also identified several TFs .