Table 1.
Differentially expressed genes at 2 and 4 months compared with 1 month in common between microarray and RNAseq analysis
| Gene symbol | RefSeq | Entrez gene name | Microarray |
RNAseq |
||
|---|---|---|---|---|---|---|
| FC 2 versus 1 | FC 4 versus 1 | FC 2 versus 1 | FC 4 versus 1 | |||
| Immune response | ||||||
| Cxcl13 | NM_018866 | Chemokine (C-X-C motif) ligand 13 | 3.01 | 1.82 | 8.32 | 4.32 |
| Lcn2 | NM_008491 | Lipocalin 2 | 2.24 | 1.73 | 6.90 | 5.93 |
| Ctss | NM_021281 | Cathepsin S | 2.12 | 1.60 | 2.30 | 1.81 |
| Ifitm3 | NM_025378 | Interferon-induced transmembrane protein 3 | 2.07 | 1.43 | 2.60 | 1.39 |
| Serping1 | NM_009776 | Serpin peptidase inhibitor, clade G, member 1 | 2.04 | 2.11 | 3.27 | 2.48 |
| A2m | NM_175628 | α-2-Macroglobulin | 1.90 | 2.51 | 2.86 | 2.62 |
| Anxa1 | NM_010730 | Annexin A1 | 1.83 | 2.26 | 1.71 | 2.14 |
| Cfl | NM_007686 | Complement factor I | 1.74 | 2.01 | 3.22 | 2.45 |
| Cd93 | NM_010740 | CD93 molecule | −1.52 | −2.01 | −1.61 | −3.10 |
| Tnfsf13 | NM_023517 | Tumor necrosis factor superfamily, member 13 | −1.59 | −2.03 | −2.25 | −2.65 |
| Glmn | NM_133248 | Glomulin, FKBP-associated protein | −2.10 | −2.20 | −1.83 | −2.01 |
| Signal transduction | ||||||
| Drd4 | NM_007878 | Dopamine receptor D4 | 2.71 | 2.31 | 4.05 | 3.54 |
| Ednrb | NM_007904 | Endothelin receptor type B | 2.36 | 2.75 | 1.85 | 2.79 |
| Egfr | NM_207655 | Epidermal growth factor receptor | 1.93 | 2.15 | 1.84 | 2.47 |
| Gna14 | NM_008137 | Guanine nucleotide binding protein, α14 | 1.83 | 2.40 | 2.56 | 3.08 |
| Arrdc2 | NM_027560 | Arrestin domain containing 2 | 1.39 | 2.10 | 2.51 | 6.47 |
| Pde6b | NM_008806 | Phosphodiesterase 6B, cGMP-specific, rod, β | −1.11 | −2.08 | −1.12 | −2.26 |
| Mtnr1a | NM_008639 | Melatonin receptor 1A | −1.53 | −2.08 | −1.23 | −5.23 |
| Tnfrsf18 | NM_009400 | Tumor necrosis factor receptor superfamily, member 18 | −2.00 | −2.05 | −2.07 | −1.59 |
| Response to stress antiapoptosis visual perception | ||||||
| Crygs | NM_009967 | Crystallin, γS | −2.29 | −2.30 | −3.5E + 16 | −4.4E + 15 |
| Crygd | NM_007776 | Crystallin, γD | −2.64 | −2.33 | −7.4E + 16 | −5.7E + 15 |
| Crygc | NM_001082573 | Crystallin, γC | −2.70 | −2.78 | −7.2E + 15 | −6.2E + 15 |
| Cryba1 | NM_009965 | Crystallin, βA1 | −4.46 | −4.71 | −7.5E + 15 | −4.4E + 15 |
| Crybb1 | NM_023695 | Crystallin, βB1 | −4.95 | −4.18 | −11.34 | −15.34 |
| Cryaa | NM_013501 | Crystallin, αA | −14.55 | −14.54 | −4.4E + 15 | −4.4E + 15 |
| Regulation of transcription | ||||||
| Esrrb | NM_001159500 | Estrogen-related receptor β | 2.85 | 3.44 | 2.30 | 2.82 |
| En2 | NM_010134 | Engrailed homeobox 2 | 1.85 | 2.11 | 1.82 | 2.89 |
| Klf15 | NM_023184 | Kruppel-like factor 15 | 1.51 | 2.01 | 1.90 | 2.03 |
| Cell adhesion | ||||||
| Col6a1 | NM_009933 | Collagen, type VI, α1 | −1.88 | −2.06 | −2.79 | −2.73 |
| Cldn5 | NM_013805 | Claudin 5 | −1.90 | −2.38 | −1.55 | −2.64 |
| Metabolic process | ||||||
| Hs6st2 | NM_001077202 | Heparan sulfate 6-O-sulfotransferase 2 | 2.87 | 4.95 | 2.40 | 3.44 |
| Pnpla3 | NM_054088 | Patatin-like phospholipase domain containing 3 | −2.05 | −2.31 | −2.51 | −2.67 |
| Regulation of cell growth | ||||||
| Fam107a | NM_183187 | Family with sequence similarity 107, member A | 2.36 | 2.64 | 3.77 | 3.79 |
| Transport | ||||||
| Tc2n | NM_001082976 | Tandem C2 domains, nuclear | 2.74 | 2.65 | 8.35 | 8.38 |
| Scn7a | NM_009135 | Sodium channel, voltage-gated, type VII, α | 2.12 | 2.83 | 1.85 | 2.30 |
| Unknown | ||||||
| Fam159b | NM_029984 | Family with sequence similarity 159, member B | 2.10 | 3.10 | 2.43 | 5.30 |
| Samd7 | NM_029489 | Sterile α motif domain containing 7 | 2.09 | 1.69 | 2.02 | 1.81 |
| Agxt2l1 | NM_027907 | Alanine-glyoxylate aminotransferase 2-like 1 | 2.06 | 2.73 | 1.61 | 2.44 |
| Acrbp | NM_016845 | Acrosin binding protein | −2.35 | −2.28 | −2.11 | −1.97 |
Microarray analysis identified 88 genes with FC2 differentially expressed between 2 and 4 months compared with 1 month. Among them, 39 were present in RNAseq data analysis. These genes are potentially involved in the transient cell death occurring in Nrl−/− retina between 1 and 4 months of age.