Table 2. Candidate photoreceptor genes (CPGs) resulting from the guilty-by-association analysis of the gene co-expression network.
| Gene | FDR | Expr. rank | Comment | Neighbour GO Enrichment |
|---|---|---|---|---|
| DPYSL3 | 6.25E-21 | 184 | Neurite and axonal outgrowth | Visual perception |
| Photoreceptor outer segment | ||||
| Photoreceptor activity | ||||
| C2orf71 | 4.05E-19 | 1041 | Retinitis Pigmentosa 54 | Fatty acid elongation, polyunsaturated f… |
| Calcineurin complex | ||||
| Fatty acid elongase activity | ||||
| CPLX4 | 8.37E-18 | 380 | Expressed in mouse rod cells | Chaperone-mediated protein complex assem… |
| Phagolysosome membrane | ||||
| Lipid transporter activity | ||||
| GSKIP | 1.16E-17 | 4593 | Potentially involved in photoreceptor cell survival | Visual perception |
| Photoreceptor disc membrane | ||||
| 3′,5′-cyclic-nucleotide phosphodiesteras… | ||||
| ANO2* | 1.42E-16 | 320 | Potentially involved in photoreceptor membrane potential and firing | Detection of light stimulus |
| Photoreceptor outer segment | ||||
| Potassium ion transmembrane transporter … | ||||
| WLS | 2.83E-16 | 1902 | Mediate many developmental processes during embryogenesis | Detection of light stimulus |
| Photoreceptor outer segment membrane | ||||
| Voltage-gated potassium channel activity | ||||
| GPR160 | 7.59E-16 | 2794 | G-protein coupled receptor with unknown function | Visual perception |
| Nonmotile primary cilium | ||||
| Mannosyl-oligosaccharide 1,3-1,6-alpha-m… | ||||
| PAIP2B | 1.63E-15 | 3730 | Influence membrane potential and light-dependent firing | Visual perception |
| Cilium | ||||
| Calmodulin binding | ||||
| TMEM136 | 2.05E-15 | 2088 | Transmembrane protein is expressed in mouse neuroretina | Cellular potassium ion transport |
| Calcineurin complex | ||||
| Voltage-gated potassium channel activity | ||||
| AGPAT3 | 3.47E-15 | 243 | Ubiquitous acetyltransferase involved in lipid metabolism | Visual perception |
| Photoreceptor outer segment | ||||
| Voltage-gated potassium channel activity | ||||
| PAQR4* | 3.89E-15 | 673 | Structurally similar to ADIPOR1 and ADIPOR2 | Visual perception |
| Photoreceptor disc membrane | ||||
| 3′,5′-cyclic-gmp phosphodiesterase activ… | ||||
| LMOD1 | 6.39E-15 | 1440 | Muscular antigen involved in Thyroid Ophthalmopathy | Visual perception |
| Photoreceptor outer segment | ||||
| Biotinidase activity | ||||
| MEF2C | 7.03E-15 | 5685 | TF involved in multi-organs development including brain | Visual perception |
| Cilium | ||||
| Calmodulin binding | ||||
| LAPTM4B* | 1.49E-14 | 299 | Lysosome-associated protein expressed in many tissues | Visual perception |
| Cilium | ||||
| Retinal binding |
Only genes ranked in the top 15 positions according to their significance in the guilty-by-association analysis are shown (for the full list refer to Supplementary Table S13). FDR: false discovery rate. Expr. Rank: rank of the gene in the retina with respect to its expression level (e.g. 1 being the most expressed). Comment: a manual-curated comment obtained by querying OMIM, PubMed and MGI. Neighbour GO Enrichment: the most enriched GO term among the genes’ neighbours in the co-expression network.