Alteration in ganglioside composition in F-11 cells by suppression of GD3-synthase gene expression resulted in greatly reduced tumor growth and metastasis when the cells were injected into nude mice. To identify genes whose expression is correlated with the decreased level of ganglioside GD3, we analyzed gene expression profiles of the GD3-suppressed F-11 cells and the control F-11 cells using DNA microarrays. We identified a set of GD3-related genes, most of which are involved in tumor growth and development. The genes that define the proliferation-transformation signature are down-regulated, such as creatine kinase-B (CKB), upstream stimulation factor 1 (USF-1), type II cAMP-dependent protein kinase regulatory subunit (RII PKA), and tyrosine hydroxylase (TH). On the other hand, the genes that define the differentiation-reverse transformation signature are up-regulated, including p160 myb-binding protein (P160), brain factor-2, insulin-like growth factor-binding protein (IGFBP), and growth/differentiation factor 11. Transcriptional levels of the genes that showed the most distinct GD3-related expression change were validated by reverse transcription-polymerase chain reaction (RT-PCR). Defining GD3-related genes may lead to identification of clinically relevant therapeutics and to understanding of the mechanism(s) by which ganglioside GD3 affects tumor growth and metastasis.