Expression profiles of genes induced by sequential treatment with BDNF in SH-SY5Y-E cells. Heat map representation is shown for genes that are down-regulated or maintained at a low level in the presence of RA but are induced by additional treatment with BDNF in SH-SY5Y-E cells. RNA sampling was performed at five time points (0 h, 6 h, 1 day, 2 days and 3 days) after cells were transferred to serum-free medium containing BDNF. To identify the gene expression induced by BDNF, we focused on genes with expression levels that were higher in SH-SY5Y-A cells during differentiation, rather than those in SH-SY5Y-E or SK-N-SH cells. We also selected genes with expression levels in SH-SY5Y-A cells treated with RA for 5 days that exceeded 66.7% of that on day 0, while excluding genes with expression levels that exceeded the 66.7% threshold in SH-SY5Y-E cells treated with RA for 5 days. We selected genes with expression levels that underwent a >1.5-fold change and exceeded the 66.7% threshold when SH-SY5Y-E cells were treated sequentially with BDNF for 3 days. Finally, genes exhibiting similar up-regulation by BDNF in SH-SY5Y-E cells and SK-N-SH cells were also excluded. Genes regulated by the PI3K signalling pathway in RA-treated SH-SY5Y-A cells (left panel) and genes not regulated by the PI3K signalling pathway in SH-SY5Y-A cells (right panel) are shown. The relative alteration of gene expression in these gene pools is summarised in Additional file 1. Genes involved in neural processes are shown in red, and those expressed strongly in brain are shown in purple. Genes encoding transcription factors are underlined.