Differently expressed genes between the control, syngeneic and allogeneic group. Class comparisons were performed using BRB array tools to identify genes with significant changes in expression levels between the syngeneic group (sTX_con) or the allogeneic group (aTX_con) compared to the control group and between allogeneic and syngeneic group (aTX_sTX; Fig. 2A). Genes with a p-value < 0.001 were classified as significant regulated. The complete lists with the significant regulated genes are provided with this manuscript (see additional file 1). The Venn diagram in Fig. 2B shows the number of overlapping genes. The changes in expression compared to control for selected genes were analyzed by real time PCR using specific primer pairs or TaqMan gene expression assays. Relative changes were evaluated using the 2-ΔΔCt method. The changes in gene expression after allogeneic transplantation are shown in Fig. 2C and the results for the syngeneic transplantation group in Fig. 2D. The black columns show the corresponding expression levels on the arrays (ratio of mean signal intensities). MMP7. IL10, C4bpa, Tap1 and Tap2 were not differently expressed after syngeneic transplantation on the array. There was no corresponding probe set for FoxP3 on the array.