Table 1.

Gene expression pattern differences between ChIA-PET CTCF loop-enclosed, loop-flanking and loop-distal genes

Cell line	Measure	Loops	Flanks	Distal	Flanks/Loops		Flanks/Distal		Loops/Distal
					FCa	P-valueb	FC	P-value	FC	P-value
K562	Gene Count	4378	4767	6466
	Median Expression (FPKM)c	0.853	1.698	0.091	1.99	5.89e–07	18.66	1.25e–93	9.37	9.74e–56
	Median TSId	0.754	0.6756	0.7565	0.9	5.3e–37	0.89	8.23e–47	1.0	0.27
	Median CVe	1.142	0.8357	1.192	0.73	1.72e–36	0.7	1.34e–56	0.96	0.01
MCF7	Gene Count	5469	6490	3847
	Median Expression (FPKM)	0.467	2.18	0.413	4.67	1.92e–65	5.28	1.07e–90	1.13	9.04e–06
	Median TSI	0.7818	0.6721	0.7549	0.86	1.65e–98	0.89	3.16e–46	1.04	1.19e–05
	Median CV	1.331	0.8214	1.178	0.62	3.92e–100	0.7	9.91e–56	1.13	7.65e–04

^aFC: Fold Change of the medians

^b P-value based on Wilcoxon rank sum test with continuity correction

^cFPKM: Fragments Per Kilobase per Million mapped reads

^dTSI: Tissue Specificity Index

^eCV: Coefficient of Variation