Figure 3.

Gene expression analysis of Pax2/8 mutant kidneys. (A) Volcano plot of Affymetrix gene array comparisons between control (n=3) and Pax2/8 KOs (n=3) using total kidney RNA. (B) Heat map and clustering of 241 genes downregulated (blue) and 466 genes upregulated (red) in Pax2/8 KOs. Gene symbols and fold change are available in Supplemental Table 1. (C) Heat map of genes encoding the solute carrier family of transmembrane transporters that are downregulated in Pax2/8 KOs. (D) Gene Ontology analyses of genes downregulated in Pax2/8 KOs, using the Toppgene suite.²⁵ The gene list reduced in KOs shows strong correlation with ion transporters and urine concentration. (E) Common transcription factor motifs (TFs) found in the genes downregulated in Pax2/8 KOs and in genes upregulated in Pax2/8 KOs. The top 5 TFs are shown, the most significant by far being the Pax2 family found in genes downregulated. The Pax2 DNA-binding matrix common to most genes downregulated in the mutants is shown. V$IRFF, interferon regulatory factors; V$MYT1, C2H2 zinc finger proteins; V$SORY, Sox/Sry HMG Box proteins; V$SP1F, GC-Box factor Sp1; V$ZFHX, Zinc Finger homeodomain.