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Table 1 Gene expression pattern differences between ChIA-PET CTCF loop-enclosed, loop-flanking and loop-distal genes

From: CTCF-mediated chromatin loops enclose inducible gene regulatory domains

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
  1. aFC: Fold Change of the medians
  2. b P-value based on Wilcoxon rank sum test with continuity correction
  3. cFPKM: Fragments Per Kilobase per Million mapped reads
  4. dTSI: Tissue Specificity Index
  5. eCV: Coefficient of Variation