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Seventy-seven genes significantly differentiated between these two experimental groups. Of them, the two most downregulated were spastic paraplegia 21 (human) homolog ( Spg21) and 6-pyruvoyl-tetrahydropterin synthase ( Pts) genes. Since the targeted mutagenesis of the \u03b24 nAChR subunit was done by using two mouse strains, 129SvEv and C57BL\/6J, it is possible that the genes closely linked to the mutated \u03b24 gene represent the 129SvEv allele and not the control C57BL\/6J-driven allele. We examined this possibility by using public database and quantitative RT-PCR. The expression levels of Spg21 and Pts genes that, like the \u03b24 gene, are localized on mouse chromosome 9, as well as the expression levels of other genes located on this chromosome, were dependent on the mouse background strain. The 67 differentially expressed genes that are not located on chromosome 9 were further analyzed for overrepresented functional annotations and transcription regulatory elements compared with the entire microarray. Genes encoding for proteins involved in tyrosine phosphatase activity, calcium ion binding, cell growth and\/or maintenance, and chromosome organization were overrepresented. Our data enhance the understanding of the molecular interactions involved in the \u03b24 nAChR subunit function. 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