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Table 3 Fold-change (\(\log _{2}\)) between bilateral regions (500kb) and TAD boundary segments (1kb) for 10 regulatory functional elements over normalized interaction dataset of 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 0.318 0.307 0.285 − 0.269 0.324 0.191 0.389 0.038 0.383 0.359 17
Arrowhead 0.609 0.391 0.372 − 0.356 0.473 0.220 0.695 0.185 0.646 0.557 27
CaTCH 0.549 0.706 0.731 − 0.659 0.813 0.522 0.568 0.127 0.471 0.813 31
Constrained HAC 0.873 0.527 0.663 − 0.409 0.502 0.358 1.062 0.132 0.999 0.785 33
CHDF 0.481 0.363 0.352 − 0.226 0.309 0.265 0.606 0.036 0.613 0.412 23
ClusterTAD 0.515 0.452 0.495 − 0.474 0.478 0.299 0.598 0.032 0.543 0.577 25
deDoc 0.608 0.314 0.293 − 0.284 0.243 0.183 0.773 0.035 0.745 0.420 20
DI 0.644 0.630 0.616 − 0.438 0.654 0.439 0.714 0.146 0.646 0.721 33
EAST 0.292 0.109 0.233 − 0.077 0.260 0.110 0.372 0.039 0.365 0.062 15
GMAP 0.432 0.291 0.395 − 0.351 0.462 0.292 0.433 0.159 0.381 0.568 24
GRiNCH 0.434 0.294 0.396 − 0.352 0.464 0.295 0.436 0.160 0.382 0.569 24
HiCExplorer 0.696 0.452 0.372 − 0.365 0.332 0.226 0.852 0.082 0.804 0.533 27
HiCKey 0.697 0.454 0.373 − 0.369 0.335 0.228 0.850 0.081 0.802 0.531 27
HiCseg 0.669 0.670 0.699 − 0.405 0.753 0.417 0.689 0.175 0.595 0.810 34
IC-Finder 0.532 0.505 0.424 − 0.286 0.408 0.307 0.635 0.096 0.597 0.521 26
InsulationScore 0.274 0.254 0.201 − 0.329 0.394 0.281 0.339 0.178 0.282 0.328 20
Matryoshka 0.365 0.384 0.347 − 0.295 0.394 0.276 0.460 0.075 0.430 0.410 21
MrTADFinder 0.123 − 0.021 0.004 − 0.136 0.047 − 0.042 0.121 0.004 0.098 0.162 9
MSTD 0.491 0.195 0.197 − 0.489 0.243 0.115 0.568 0.111 0.463 0.499 22
OnTAD 0.603 0.428 0.374 − 0.343 0.418 0.273 0.717 0.117 0.689 0.459 26
Spectral 0.041 0.069 − 0.064 0.010 0.108 − 0.045 0.052 − 0.004 0.045 0.046 9
SpectralTAD 0.544 0.425 0.410 − 0.230 0.361 0.221 0.669 0.057 0.634 0.491 24
TADBD 0.213 0.151 0.139 − 0.124 0.191 0.122 0.248 0.117 0.246 0.163 13
TADbit 0.598 0.591 0.642 − 0.377 0.632 0.424 0.657 0.165 0.572 0.747 33
TADpole 0.325 0.327 0.254 − 0.121 0.298 0.199 0.387 0.079 0.380 0.295 18
TADtree 0.323 0.325 0.256 − 0.124 0.297 0.196 0.385 0.077 0.381 0.293 18
TopDom 0.673 0.445 0.353 − 0.382 0.311 0.237 0.830 0.062 0.793 0.505 27
  1. The final column is sum of each caller’s ranking in terms of the whole set of functional regulatory elements except H3K9me3. Bold numbers show the leading result for every column