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Table 2 The mean peak near inferred TAD boundaries (2kb) for 10 functional elements over normalized interaction dataset from human embryonic stem cells 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 0.253 0.333 0.337 0.367 0.085 0.646 0.155 4.542 0.144 0.338 16
Arrowhead 0.333 0.401 0.419 0.458 0.108 0.715 0.211 5.366 0.194 0.418 28
CaTCH 0.230 0.371 0.399 0.238 0.101 0.650 0.141 3.701 0.126 0.372 14
Constrained HAC 0.397 0.451 0.515 0.376 0.111 0.782 0.271 5.199 0.243 0.503 33
CHDF 0.280 0.339 0.352 0.387 0.084 0.652 0.181 4.482 0.169 0.344 17
ClusterTAD 0.321 0.471 0.505 0.362 0.118 0.832 0.203 5.148 0.187 0.490 31
deDoc 0.345 0.401 0.412 0.416 0.098 0.717 0.229 5.036 0.213 0.406 27
DI 0.375 0.533 0.558 0.383 0.139 0.916 0.238 5.678 0.216 0.512 36
EAST 0.258 0.362 0.388 0.452 0.094 0.694 0.163 4.618 0.153 0.309 17
GMAP 0.287 0.353 0.411 0.413 0.101 0.778 0.174 5.283 0.160 0.420 23
GRiNCH 0.291 0.357 0.415 0.414 0.100 0.775 0.176 5.285 0.158 0.423 23
HiCExplorer 0.393 0.466 0.461 0.417 0.111 0.774 0.258 5.372 0.236 0.463 33
HiCKey 0.332 0.475 0.501 0.344 0.123 0.772 0.197 5.157 0.181 0.490 31
HiCseg 0.330 0.472 0.504 0.347 0.125 0.770 0.201 5.153 0.178 0.489 31
IC-Finder 0.343 0.460 0.458 0.430 0.112 0.790 0.218 5.359 0.201 0.446 28
InsulationScore 0.275 0.365 0.376 0.377 0.101 0.751 0.175 5.429 0.162 0.366 21
Matryoshka 0.274 0.388 0.390 0.365 0.098 0.737 0.173 4.926 0.158 0.370 20
MrTADFinder 0.215 0.248 0.269 0.429 0.067 0.506 0.126 4.354 0.116 0.297 10
MSTD 0.289 0.341 0.358 0.381 0.089 0.656 0.181 4.959 0.159 0.396 20
OnTAD 0.377 0.485 0.479 0.420 0.123 0.826 0.250 5.622 0.231 0.455 35
Spectral 0.191 0.247 0.247 0.419 0.067 0.474 0.118 4.078 0.109 0.246 9
SpectralTAD 0.311 0.384 0.411 0.426 0.095 0.676 0.208 4.840 0.189 0.388 24
TADBD 0.294 0.375 0.387 0.456 0.101 0.724 0.182 5.503 0.172 0.352 21
TADbit 0.361 0.520 0.558 0.410 0.133 0.888 0.224 5.647 0.201 0.522 34
TADpole 0.287 0.392 0.390 0.454 0.105 0.725 0.179 5.146 0.165 0.369 21
TADtree 0.284 0.396 0.392 0.453 0.101 0.722 0.177 5.145 0.167 0.367 21
TopDom 0.382 0.467 0.458 0.387 0.110 0.785 0.252 5.316 0.234 0.448 32
  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