Table 9. Top 25 transcripts upregulated in Nrl−/− retina compared to WT.
| Transcript | Gene ID | Gene title | WT FPKM | Nrl−/− FPKM | FC |
|---|---|---|---|---|---|
|
NM_021272 |
Fabp7 |
Fatty acid binding protein 7 brain |
2.5 |
62.7 |
24.59 |
|
NM_007538 |
Opn1sw |
Opsin 1 short-wave-sensitive |
149.1 |
2740.1 |
18.38 |
|
NM_013927 |
Cngb3 |
Cyclic nucleotide gated channel β 3 |
4.7 |
85.6 |
18.13 |
|
NM_033614 |
Pde6c
(isoform 1) |
Phosphodiesterase 6C, cGMP-specific, cone, α prime |
12.6 |
199.5 |
15.78 |
|
NM_001170959 |
Pde6c
(isoform 2) |
Phosphodiesterase 6C, cGMP-specific, cone, α prime |
13.8 |
207.9 |
14.93 |
|
NM_001038664 |
Gngt2
(isoform 2) |
Guanine nucleotide binding protein γ transducing activity polypeptide 2 |
22.6 |
337.8 |
14.93 |
|
NM_001166651 |
Klhl33 |
Kelch-like 33 |
3 |
42.2 |
14.03 |
|
NM_007627 |
Cckbr |
Cholecystokinin B receptor |
3.6 |
50.2 |
13.83 |
|
NM_017474 |
Clca3 |
Chloride channel calcium activated 3 |
3.4 |
46.2 |
13.64 |
|
NM_027132 |
Otop3 |
Otopetrin 1 homolog |
4.4 |
56.5 |
12.82 |
|
NM_023121 |
Gngt2
(isoform 1) |
Guanine nucleotide binding protein γ transducing activity polypeptide 2 |
32 |
407.3 |
12.73 |
|
NM_178747 |
Gulo |
L gulonolactone oxidase |
6.5 |
82.7 |
12.64 |
|
NM_008141 |
Gnat2 |
Guanine nucleotide binding protein γ transducing activity polypeptide 2 |
70.5 |
861.1 |
12.21 |
|
NM_145574 |
Ccdc136 |
Coiled-coil domain containing 136 |
17.6 |
213.8 |
12.13 |
|
NM_009918 |
Cnga3 |
Cyclic nucleotide gated channel α 3 |
5 |
54.6 |
11 |
|
NM_133205 |
Arr3 |
Arrestin 3, retinal |
69.6 |
652.6 |
9.32 |
|
NM_184053 |
Calu |
Calumenin, a calcium ion binding protein |
14.8 |
131.6 |
8.82 |
|
NM_183224 |
Fam19a3 |
Family with sequence similarity 19, member A3 |
30.7 |
266.9 |
8.69 |
|
NM_010164 |
Eya1 |
Eyes absent 1 homolog |
1.4 |
12.6 |
8.63 |
|
NM_001201378 |
Ccdc136 |
Coiled-coil domain containing 136 |
16.6 |
142 |
8.51 |
|
NM_025659 |
Abi3 |
ABI gene family, member 3 |
1.4 |
11.5 |
8.28 |
|
NM_013848 |
Ermap |
Erythroblast membrane-associated protein |
1.2 |
9.8 |
8 |
|
NM_133167 |
Parvb |
Parvin β |
9 |
71.5 |
7.94 |
|
NM_007419 |
Adrb1 |
Β-1 adrenergic receptor |
6.5 |
50.2 |
7.73 |
| NM_138653 | Bspry | B-box and SPRY-domain containing (zetin-1) | 1.4 | 10.6 | 7.73 |
Many of the genes down-regulated in Nrl−/− retina represent rod-specific transcripts, whereas upregulated genes include those associated with cone function and retinal remodeling.