Figure 2. Measures of differential gene expression. Microarray data are indicated by blue bars and QRT–PCR data by red bars. We selected differentially regulated genes (*p<0.01) identified by the microarray, binding partners of those differentially regulated genes, as well as five other relevant genes of interest: SEMA3G, FGF2, VEGF, and ephrin-A2 and -A3. A, B: Selected axonal guidance genes. These genes were significantly upregulated or downregulated in the macula compared to either the nasal (A) or surround (B) samples, with the exception of SEMA3G, which was significantly upregulated only in the macula versus surround comparison (B). C: QRT–PCR indicates strong differential regulation of Eph-A6 and its ligands ephrin-A1 and -A4 in the macula compared with nasal samples. The QRT–PCR results showed stronger trends in differential expression compared to the microarray, with the exception of ephrin-A3, which QRT–PCR suggests is not differentially expressed. Similar data were obtained from macula versus surround comparisons. D: The QRT–PCR confirmed significant upregulation of PEDF and NPPB in the macula compared with the nasal sample. Both the microarray and QRT–PCR findings indicate no differential regulation of VEGFA, the major isoform expressed in the retina. The small downregulation of FGF2 in the microarray and QRT–PCR data are consistent with our previous findings that show a downregulation of FGF2 in macular cones, but not in other layers of the retina, by in situ hybridization [32]. Note that the standard error of the microarray fold changes is derived from the distribution of fold changes measured across the four specimens. Abbreviations: fibroblast growth factor 2 (FGF2); natriuretic peptide precursor B (NPPB); neuropilin 1 (NRP1); netrin G1 (NTNG1); pigment epithelium derived factor (PEDF); plexin C1 (PLXNC1); semaphorin 3D (SEMA3D); semaphorin 3G (SEMA3G); semaphorin 4F (SEMA4F); unc-5 homolog D (C. elegans; UNC5D); vascular endothelial growth factor A (VEGFA).