Table 2.
Non-redundant differentially expressed genes in Crxp-Nrl/WT or Crxp-Nr2e3/WT samples compared to Nrl−/− retinas. Gene profiles of P28 retinal samples from Crxp-Nrl/WT or Crxp-Nr2e3/WT were compared to the profiles from the Nrl−/− retina. We show common differentially expressed genes in Crxp-Nrl/WT and Crxp-Nr2e3/WT retina, or unique genes from Crxp-Nrl/WT or Crxp-Nr2e3/WT, with a minimum fold change of 10 and FDRCI P-value of < 0.1. AFC, average fold change.
| Gene Symbol | Gene Title | AFC Crxp-Nrl/WT versus Nrl−/− | AFC Crxp- Nr2e3/WT versus Nrl−/− | GO biological process description |
|---|---|---|---|---|
| Overlapping genes in Crxp-Nrl/WT and Crxp-Nr2e3/WT versus Nrl−/− group | ||||
| Nrl | Neural retina leucine zipper gene | 386.9 | 381.8 | Photoreceptor cell development |
| Rho | Rhodopsin | 347.1 | 332.5 | Phototransduction |
| Nr2e3 | Nuclear receptor subfamily 2, group E, member 3 | 115.8 | 83.9 | Photoreceptor cell development |
| Gnb1 | Guanine nucleotide binding protein, beta 1 | 69.7 | 46.1 | Phototransduction |
| Slc24a1 | Solute carrier family 24 (sodium/potassium/calcium exchanger), member 1 | 50.9 | 43.3 | Calcium ion transport/visual perception |
| A930036K24Rik | RIKEN cDNA A930036K24 gene | 50.1 | 88.7 | |
| BC016201 | cDNA sequence BC016201 | 40.8 | 33.8 | |
| Esrrb | Estrogen related receptor, beta | 32.4 | 26.9 | Intracellular protein transport |
| Susd3 | Sushi domain containing 3 | 23.4 | 21.5 | |
| Aqp1 | Aquaporin 1 | 21.3 | 31.4 | Water transport |
| BC038479 | cDNA sequence BC038479 | 20.4 | 17.5 | |
| Reep6 | Receptor accessory protein 6 | 17.9 | 20.9 | Protein binding |
| Mef2c | Myocyte enhancer factor 2C | 16.7 | 10.8 | Regulation of transcription |
| Pde6b | Phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide | 16.7 | 19.4 | Activation of MAPK activity/Visual perception |
| Wisp1 | WNT1 inducible signaling pathway protein 1 | 16.1 | 20.3 | Regulation of cell growth |
| Sh2d1a | SH2 domain protein 1A | 15.8 | 18.7 | Intracellular signaling cascade |
| Sgcg | Sarcoglycan, gamma (dystrophin-associated glycoprotein) | 14.6 | 10.6 | Cytoskeleton organization and biogenesis |
| Samd11 | Sterile alpha motif domain containing 11 | 13.9 | 16.5 | Negative regulation of transcription |
| Plekha2 | Pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2 | 11.4 | 14.7 | Phosphatidylinositol binding |
| Vax2os1 | Vax2 opposite strand transcript 1 | 10.3 | 15.6 | |
| Guca1b | Guanylate cyclase activator 1B | 10.2 | 10.6 | Phototransduction |
| Gulo | Gulonolactone (L-) oxidase | −10.0 | −31.3 | L-ascorbic acid biosynthetic process |
| Pik3ap1 | Phosphoinositide-3-kinase adaptor protein 1 | −11.1 | −11.3 | Transmembrane receptor protein tyrosine kinase signaling protein activity |
| Gngt2 | Guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 2 | −11.7 | −11.9 | G-protein coupled receptor protein signaling pathway |
| En2 | Engrailed 2 | −12.0 | −10.4 | Regulation of transcription |
| Myocd | Myocardin | −12.5 | −12.7 | Regulation of cell growth |
| Kcne2 | Potassium voltage-gated channel, Isk-related subfamily, gene 2 | −12.7 | −12.4 | Potassium ion transport |
| Arhgdib | Rho, GDP dissociation inhibitor (GDI) beta | −13.8 | −12.8 | Rho GDP-dissociation inhibitor activity |
| Parvb | Parvin, beta | −13.9 | −14.0 | Actin binding |
| Cckbr | Cholecystokinin B receptor | −17.4 | −33.3 | G-protein coupled receptor protein signaling pathway |
| Klhl4 | Kelch-like 4 (Drosophila) | −19.8 | −17.4 | |
| A930009A15Rik | RIKEN cDNA A930009A15 gene | −24.4 | −28.9 | |
| Otop3 | Otopetrin 3 | −39.2 | −39.3 | |
| Cngb3 | Cyclic nucleotide gated channel beta 3 | −40.8 | −49.4 | Potassium ion transport |
| Gnat2 | Guanine nucleotide binding protein, alpha transducing 2 | −46.0 | −56.2 | Phototransduction |
| Fabp7 | Fatty acid binding protein 7, brain | −60.1 | −48.8 | Lipid binding |
| Opn1mw | Opsin 1 (cone pigments), medium-wave- sensitive (color blindness, deutan) | −77.9 | −76.2 | Phototransduction |
| Clca3 | Chloride channel calcium activated 3 | −91.6 | −93.5 | Chloride transport |
| Pde6c | Phosphodiesterase 6C, cGMP specific, cone, alpha prime | −158.3 | −136.8 | Activation of MAPK activity/visual perception |
| Arr3 | Arrestin 3, retinal | −271.2 | −166.0 | Regulation of phosphorylation |
| Pde6h | Phosphodiesterase 6H, cGMP-specific, cone, gamma | −429.1 | −409.3 | Activation of MAPK activity/visual perception |
| Opn1sw | Opsin 1 (cone pigments), short-wave- sensitive (color blindness, tritan) | −559.2 | −546.8 | Phototransduction |
| Unique genes in Crxp-Nrl/WT versus Nrl−/− group | ||||
| Rds | Retinal degeneration, slow (retinitis pigmentosa 7) | 149.7 | 3.3 | Sensory perception of light stimulus |
| Stk35 | Serine/threonine kinase 35 | 11.7 | 2.3 | Protein amino acid phosphorylation |
| Mtmr7 | Myotubularin related protein 7 | −11.8 | 1.8 | Phospholipid dephosphorylation |
| Pcdh15 | Protocadherin 15 | −12.6 | −3.3 | Sensory perception of light stimulus |
| Pip5k2b | Phosphatidylinositol-4-phosphate 5-kinase, type II, beta | −12.6 | 1.3 | Glycerophospholipid metabolic process |
| Unique genes in Crxp-Nr2e3/WT versus Nrl−/− group | ||||
| A930003C13Rik | RIKEN cDNA A930003C13 gene | 3.5 | 11.5 | |
| Skiv2l2 | Superkiller viralicidic activity 2-like 2 (S. cerevisiae) | −4.4 | −17.0 | RNA splicing |