Molecular Vision: Hoang, Mol Vis 2014; 20:1491-1517. Table 5

Table 5. Expression of genes encoding DNA degradation enzymes and genes involved in DNA repair.

Gene function	Gene symbol	Description	F_RPKM	E_RPKM	F_counts	E_counts	FC*	P value
DNases	Dnase2b	DNase II beta	34.89	1.00	2539.30	25.21	100.73	1.42E-176
	Dnase2a	DNase II alpha	2.27	10.00	39.87	64.31	−1.61	0.297074881
	Dnase1	DNase I	1.94	2.81	43.39	43.67	−1.01	1
DNA repairs	Lig3	Ligase III, DNA	6.27	17.17	540.75	492.46	1.10	1
	H2afx	H2A histone family, member X	5.64	44.44	217.55	601.89	−2.77	2.35E-10
	Rad52	RAD52 homolog	3.69	18.37	98.93	197.52	−2.00	0.006096111
	Mre11a	Meiotic recombination 11 homolog A	3.26	7.88	255.29	205.85	1.24	0.495213491
	Lig1	Ligase I, DNA	2.18	34.39	59.61	392.69	−6.59	0.001185211
	Lig4	Ligase IV, DNA	1.41	1.70	160.55	66.73	2.41	0.003428077
	Rad50	RAD50 homolog	1.34	4.20	98.11	208.59	−2.13	0.03211083
	Nbn	Nibrin	1.09	9.82	77.74	255.87	−3.29	0.000000271
	Mdc1	Mediator of DNA damage checkpoint 1	1.00	5.60	104.95	346.84	−3.30	0.000375043
	Atm	Ataxia telangiectasia mutated homolog	0.99	6.17	176.91	272.31	−1.54	0.047464437
	Chek1	Checkpoint kinase 1 homolog	0.64	10.24	10.16	102.10	−10.05	1.92E-09
	Brca1	Breast cancer 1	0.42	1.87	65.72	104.73	−1.59	0.462151787
	Rad51	RAD51 homolog	0.27	4.07	10.52	85.09	−8.09	0.000000624
	Brca2	Breast cancer 2	0.21	1.38	63.81	142.65	−2.24	0.174088223

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 indicated 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.