. Author manuscript; available in PMC: 2019 Apr 30.

Published in final edited form as: Hum Genet. 2018 Apr 30;137(4):315–328. doi: 10.1007/s00439-018-1884-1

Table 2.

Results from whole transcriptome analysis (RNA-Seq) and qRT-PCR results showing selected genes with significantly altered expression in foxe3 indel mutant larvae with eye defects compared to wildtype larvae

Gene/transcript	Expression	RNA-Seq log2 fold_change wildtype: mutant)	p value^*	qRT-PCR ΔΔCT^a	p value^*^b	Function	Phenotype associated with human orthologue
Downregulated
mipa/NM_001003534.1	Eye/lens fibers	−2.2	0.00005^*	2.949	0.038^*	Lens transparency	Cataract
fmodb/XM_001337991.3	Limbus/cornea	−2.12	0.00005^*	1.733	0.002	Regulation of collagen fibrillinogenesis	Unknown
cx43.4/NM_131069	Lens epithelium/fiber cells	−0.57	0.0014	0.849	0.002	Lens transparency; connexin-mediated communication in the lens	Cataract
Upregulated
lgsn/NM_001031674	Lens	3.35	0.00005^*	−4.316	0.006^*	Chaperone	Unknown
cryba2a/NM_001002049	Lens	1.3	0.00005^*	−1.655	0.034^*	Lens transparency	Cataract
cryba1l1/NM_001017738	Lens	1.07	0.0006^*	−1.674	0.038^*	Lens transparency	Cataract
crygmxl2/NM_001013262	Lens	2.08	0.00005	−2.105	0.003^*	Lens transparency	Cataract
hsf4/NM_001328208.1	Lens	3.34	0.00005^*	−2.913	0.087	HSF family; DNA binding	Cataract

qRT-PCR ΔΔCT = ΔΔCT value from qRT-PCR experiments;

p value

= significance at the 0.05 level.