Table 3.

Association of CTCF binding with repetitive elements.

Repeat ID*	Repeat class/subclass*	Number of region			Odds ratio	q-value¶
		Whole genome†	ChIP-seq peak associated‡	Control§
743	LTR/Gypsy	166	96	2	58.04	1.87E-29
274	DNA/hAT-Tip100	586	489	12	49.73	9.83E-147
771	DNA/hAT-Charlie	145	59	2	35.69	2.47E-17
738	DNA/hAT-Charlie	187	92	4	27.82	7.92E-26
697	LTR/Gypsy	359	137	7	23.70	6.85E-37
239	Unknown	1509	470	26	22.06	2.26E-124
749	DNA/hAT-Charlie	198	45	3	18.13	8.70E-12
828	SINE/tRNA-V	602	59	4	17.83	2.65E-15
337	Unknown	1553	345	24	17.50	9.98E-87

^*See Materials and Methods, for repeat identification and (sub)class assignment.

^†Total number of individual repeat regions in the whole genome identified by RepeatMasker.

^‡Number of repeat regions overlapping with ChIP-seq peaks (summit ± 50 bp).

^§Number of repeat regions overlapping with control regions (50,000 regions of 100 bp each).

^¶ p-values from Fisher’s exact test subjected to multiple correction by the Q-value package in R.