Molecular Vision: Hoang, Mol Vis 2014; 20:1491-1517. Table 3

Table 3. Expressions of genes involved in Notch signaling in epithelial cells and fiber cells.

Gene function	Gene symbol	Description	F_RPKM	E_RPKM	F_counts	E_counts	FC*	P value
Receptors	Notch1	Notch gene homolog 1	2.84	12.25	333.87	910.85	−2.73	3.83E-12
	Notch3	Notch gene homolog 3	1.28	26.82	276.06	2084.18	−7.55	1.78E-52
	Notch2	Notch gene homolog 2	0.83	30.55	243.54	3164.57	−12.99	1.48E-42
	Notch4	Notch gene homolog 4	0.13	6.98	17.67	187.21	−10.60	3.66E-13
Ligands	Jag1	Jagged 1	77.73	109.40	11,686.66	5515.88	2.12	1.07E-09
	Jag2	Jagged 2	0.78	6.39	92.41	271.70	−2.94	0.00000087
	Dll3	Delta-like 3	0.20	0.45	8.33	9.42	−1.13	1
	Dll4	Delta-like 4	0.14	2.95	11.29	113.43	−10.04	0.035633554
	Dll1	Delta-like 1	0.06	1.72	1.59	43.01	−27.09	0.00000467
Mediators/ Effectors	Herpud1	Herpud family member 1	21.57	19.77	992.83	363.88	2.73	2.84E-10
	Herpud2	HERPUD family member 2	6.09	14.73	476.03	409.29	1.16	0.844553336
	Hes6	Hairy and enhancer of split 6	4.45	25.84	141.54	358.37	−2.53	0.0000121
	Hes1	Hairy and enhancer of split 1	2.18	40.05	50.54	559.74	−11.08	6.13E-18
	Rbpj	Recombination signal binding protein for immunoglobulin kappa J region	0.35	1.36	56.67	117.19	−2.07	0.029792975
	Hes5	Hairy and enhancer of split 5	0.18	10.49	5.50	113.62	−20.66	0.0000279
	Hes7	Hairy and enhancer of split 7	0.01	0.55	0.49	10.79	−22.22	0.087807157
	Hes2	Hairy and enhancer of split 2	0.00	0.11	0.00	0.62	NA	1
	Hes3	Hairy and enhancer of split 3	0.00	0.04	0.00	0.66	NA	1
Inhibitor	Numb	Numb gene homolog	0.67	4.38	56.67	117.19	−2.07	0.029792975

Genes were ranked based on the RPKM (Reads Per Kilobase per Million mapped reads) values in the fiber cells (F) with F counts and E counts representing normalized read counts from DESeq software from the fiber and epithelial cell samples, respectively. *Fold-change (FC) was based on the expression level in the fiber cells relative to the epithelial cells in normalized counts produced by DESeq. Negative values indicate expression lower in the fiber cells compared with the epithelial cells. Genes with a p-adjusted value less than 0.05 and more than a 1.5 fold-change in normalized read counts were considered as differential expression.