For brain tissue and cell types, RFX1, 3, 4 and 7 clustered tightly together, indicating a preference for these RFX family members to (co-) regulate the expression of brain-specific genes such as the ciliopathy/Alström syndrome gene ALMS1, the dyslexia candidate gene KIAA0319 or the gene MAP1A. Interestingly, another member of the brain cluster, pC@RFX2 (Table 1, Additional file 2), in the context of target genes clustered separately (Fig. 2), suggesting that in the brain RFX2 regulates a distinct set of target genes. This evidence concerns the gene RFX2 and Down syndrome.