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Table 4 The inferred TAD boundaries boundary tagged ratio for 10 functional elements over normalized interaction dataset from human embryonic stem cell line at 5kb resolution

From: A comparison of topologically associating domain callers over mammals at high resolution

  H3K9me3 H3K4me3 H3K36me3 CTCF HK genes TSS SMC3 SINE RAD21 Polymerase II Rank
Armatus 0.695 0.311 0.351 0.630 0.156 0.860 0.570 0.998 0.530 0.501 18
Arrowhead 0.910 0.442 0.512 0.747 0.229 0.911 0.832 0.999 0.796 0.647 32
CaTCH 0.484 0.303 0.341 0.398 0.166 0.488 0.448 0.569 0.429 0.417 9
Constrained HAC 0.910 0.469 0.550 0.737 0.248 0.887 0.856 0.987 0.826 0.672 34
CHDF 0.733 0.338 0.383 0.647 0.161 0.849 0.624 0.978 0.590 0.513 20
ClusterTAD 0.779 0.471 0.533 0.689 0.243 0.807 0.712 0.981 0.691 0.679 29
deDoc 0.858 0.435 0.499 0.724 0.218 0.876 0.788 0.996 0.760 0.636 32
DI 0.920 0.530 0.598 0.747 0.289 0.909 0.858 0.996 0.828 0.733 36
EAST 0.821 0.404 0.476 0.707 0.200 0.880 0.728 0.992 0.694 0.610 27
GMAP 0.848 0.416 0.482 0.699 0.214 0.883 0.740 0.996 0.704 0.628 30
GRiNCH 0.849 0.419 0.485 0.702 0.216 0.884 0.745 0.998 0.705 0.626 30
HiCExplorer 0.942 0.490 0.559 0.770 0.257 0.906 0.894 0.997 0.870 0.698 36
HiCKey 0.944 0.492 0.561 0.768 0.259 0.908 0.894 0.997 0.870 0.699 36
HiCseg 0.872 0.505 0.576 0.706 0.278 0.870 0.804 0.988 0.771 0.705 36
IC-Finder 0.890 0.476 0.535 0.739 0.239 0.902 0.819 0.999 0.789 0.669 35
InsulationScore 0.828 0.430 0.485 0.681 0.208 0.881 0.719 0.971 0.678 0.640 29
Matryoshka 0.740 0.358 0.403 0.639 0.185 0.873 0.628 0.997 0.590 0.544 22
MrTADFinder 0.702 0.294 0.348 0.704 0.130 0.857 0.567 0.998 0.529 0.508 18
MSTD 0.853 0.380 0.450 0.689 0.194 0.872 0.766 0.991 0.726 0.609 27
OnTAD 0.926 0.507 0.577 0.758 0.263 0.910 0.867 0.998 0.841 0.712 36
Spectral 0.665 0.305 0.361 0.649 0.131 0.786 0.548 0.920 0.514 0.477 15
SpectralTAD 0.834 0.399 0.464 0.703 0.200 0.881 0.754 0.998 0.721 0.601 27
TADBD 0.864 0.436 0.499 0.712 0.216 0.901 0.770 0.999 0.737 0.630 30
TADbit 0.912 0.530 0.596 0.763 0.276 0.916 0.844 0.998 0.814 0.731 36
TADpole 0.807 0.421 0.471 0.717 0.205 0.885 0.704 0.998 0.673 0.604 28
TADtree 0.805 0.419 0.470 0.716 0.204 0.883 0.703 0.998 0.671 0.600 28
TopDom 0.897 0.471 0.534 0.730 0.242 0.881 0.841 0.996 0.817 0.674 34
  1. Bold numbers show the leading result for every column. The final column is sum of each caller’s ranking in terms of the whole set of functional regulatory elements except H3K9me3