Figure 2.

Analysis of differentially expressed genes in ependymal cells from Rfx1, Rfx2 or Rfx3 deficient mice. (A) The volcano plots represent statistical significance (Y-axis, –log₁₀P-value) and fold change (X-axis, log₂ fold change) for alterations in gene expression observed in Rfx1^−/−, Rfx2^−/− or Rfx3^−/− cells relative to WT cells. Whereas only few genes exhibited significantly altered expression in Rfx1^−/− cells, numerous genes were differentially expressed in Rfx2^−/− and Rfx3^−/− cells. (B) The Venn diagrams summarize the overlaps observed between up (left) or down (right) regulated gene sets (fold change >2) in Rfx1^−/−, Rfx2^−/− or Rfx3^−/− cells. Whereas there is little overlap between genes upregulated in Rfx2^−/− and Rfx3^−/− cells (left), most genes downregulated in Rfx2^−/− cells are also downregulated in Rfx3^−/− cells (right). There is no overlap between genes that are differentially expressed in Rfx1^−/− cells and Rfx2^−/− or Rfx3^−/− cells. (C) The bar graphs show the fold changes in gene expression (log₂ fold change) observed in Rfx2^−/− (black bars) and Rfx3^−/− (grey bars) cells for the 30 genes that are downregulated most strongly in Rfx2^−/− (left) or Rfx3^−/− (right) ependymal cells. Whereas nearly all genes that are strongly downregulated in Rfx2^−/− cells are also strongly downregulated in Rfx3^−/− cells (left), the reverse is not true (right). Genes highlighted in blue contain at least one X-box motif in their promoter region (−1000 to +500 bp).