Table 1.
Selected DE Genes Related to Apoptotic/Cell Death Processes or to Mitochondria Functions or Having Relevant Vision Functions in Mutant Retinas Compared with Age-Matched Normal Retinas at 7 and 16 Weeks and in a Combined (7 and 16 Weeks) Analysis
| Gene | Name | Related Function | GO | q (%) | Change Mutant vs. Normal |
|---|---|---|---|---|---|
| Seven Weeks | |||||
| NDUFS4 | NADH dehydrogenase (ubiquinone) Fe-S protein 4 | Mitochondria | Mitochondrial electron transport; oxygen and reactive oxygen species metabolic process | 0.0 | −47.2 |
| PAX6 | Paired box 6 | Vision | Eye development; protein and DNA binding; transcription regulator activity | 0.0 | −8.6 |
| ELOVL6 | ELOVL family member 6, elongation of long chain fatty acids | Mitochondria | Transferase activity; fatty acid elongation | 0.0 | −3.4 |
| GLOD4 | Glyoxalase domain containing 4 | Mitochondria | Lyase activity | 0.0 | −3.2 |
| PRKCB | Protein kinase C, beta | Proapoptosis | Protein kinase activity; nucleotide binding | 7.0 | −16.0 |
| TUBB2C | Tubulin, beta 2C | Cell death | Nucleotide, GTP and MHC class I protein binding; gtpase activity | 7.0 | −2.8 |
| CHML | Choroideremia-like (Rab escort protein 2) | Vision | Visual perception; regulation of gtpase activity | 9.6 | −12.6 |
| SPPI | Secreted phosphoprotein 1, osteopontin | Antiapoptosis | Protein binding; cytokine activity; inflammatory response | 9.6 | −9.0 |
| CAMK2G | Calcium/calmodulin-dependent protein kinase II gamma | Cell death | Protein kinase activity; nucleotide binding | 9.6 | −5.1 |
| RBBP6 | Retinoblastoma binding protein 6 | Proapoptosis; vision | Nucleic acid and protein binding; ubiquitin-protein ligase activity | 9.6 | −4.4 |
| REEP1 | Receptor accessory protein 1 | Mitochondria; cell death | Protein insertion into membrane | 9.6 | −4.3 |
| SMYD3 | SET and MYND domain containing 3 | Antiapoptosis | Protein binding; transferase activity | 9.6 | −3.4 |
| RNF41 | Ring finger protein 41 | Proapoptosis | Protein binding; ligase activity | 9.6 | −2.8 |
| RALA | V-ral simian leukemia viral oncogene homolog A (ras related) | Cell death | Gtpase activity; protein and nucleotide binding | 9.6 | −2.6 |
| NTRK2 | Neurotrophic tyrosine kinase, receptor, type 2 | Prosurvival | Protein kinase activity; nucleotide binding | 9.6 | −2.6 |
| RDH11 | Retinol dehydrogenase 11 | Vision | Retinol dehydrogenase activity; catalytic activity | 9.6 | −2.0 |
| Sixteen Weeks | |||||
| NKAP | NFKB activating protein | Prosurvival | Transcriptional repressor | 7.5 | −68.6 |
| TARS2 | Threonyl-tRNA synthetase 2, mitochondrial | Mitochondria | Nucleotide and ATP binding; ligase activity | 7.5 | −58.3 |
| SAG | S-antigen; retina and pineal gland (arrestin) | Vision | Protein binding; signal transduction; visual perception | 7.5 | −5.7 |
| CRX | Cone-rod homeobox | Vision | DNA and protein binding; transcription factor activity; visual perception | 7.5 | −5.0 |
| SLC25A5 | Solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5 | Mitochondria; pro-survival | Protein binding; transporter activity | 7.5 | −3.9 |
| Combined Analysis | |||||
| NDUFS4 | NADH dehydrogenase (ubiquinone) Fe-S protein 4 | Mitochondria | Mitochondrial electron transport; oxygen and reactive oxygen species metabolic process | 0.0 | −37.0 |
| ACSL1 | Acyl-CoA synthetase long-chain family member 1 | Mitochondria | Nucleotide and ATP binding | 0.0 | 2.3 |
| PDE6A | Phosphodiesterase 6A, cGMP-specific, rod, alpha | Vision | Catalytic activity; visual perception | 8.0 | −3.0 |
| PPP3CA | Protein phosphatase 3, catalytic subunit, alpha isoform | Mitochondria; proapoptosis | Protein serine/threonine phosphatase activity | 8.0 | −2.3 |
| RNF41 | Ring finger protein 41 | Proapoptosis | Protein binding; ligase activity | 8.0 | −2.3 |
| ADC | Arginine decarboxylase | Mitochondria | Protein binding; lyase activity | 8.8 | 2.5 |
| HSP90AA1 | Heat shock protein 90kDa alpha, class A member 1 | Antiapoptosis; mitochondrial transport | Nucleotide binding; protein folding; response to stress | 8.8 | 2.4 |
| TFAM | Transcription factor A, mitochondrial | Mitochondria; antiapoptosis; vision | DNA binding; regulation of transcription | 8.8 | 2.3 |
| ZBTB4 | Zinc finger and BTB domain containing 4 | Proapoptosis | DNA and protein binding; regulation of transcription | 8.8 | 2.0 |
Genes are listed from the lowest to the highest q-value per time point and are reported with the change ratios and the relevant GO functions. The entire list of DE genes is available in Supplementary Table S3.