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Table 5 Analysis for the enrichment of four regulatory elements (from the left: CTCF, Housekeeping genes, RAD21, TSSs) using the KR-normalized Micro-C dataset (\(n = 38\)) from mouse ESCs at the 1kb resolution

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

TAD Callers Functional regulatory elements
CTCF HK genes RAD21 TSS Rank
Armatus 0.334/0.802/0.615/1/0.145/0.772 0.138/0.261/0.54/1/0.19/0.27 0.267/0.756/0.622/1/0.161/0.742 0.517/0.704/0.543/1/0.089/0.836 14/13/10/16/13/12
CaTCH 0.261/0.57/0.818/1/0.033/0.684 0.142/0.237/1.154/1/0.101/0.488 0.199/0.549/0.681/1/0.039/0.676 0.472/0.508/1.021/1/0.02/0.722 10/5/14/16/4/13
Constrained HAC 0.375/0.9/1.07/1/0.033/0.622 0.136/0.282/0.937/1/0.089/0.469 0.299/0.875/1.029/1/0.039/0.615 0.518/0.693/0.864/1/0.017/0.634 15/14/16/16/4/10
ClusterTAD 0.351/0.809/0.773/1/0.024/0.473 0.167/0.31/0.954/1/0.083/0.419 0.274/0.775/0.681/1/0.028/0.469 0.587/0.729/0.781/1/0.014/0.511 16/14/13/16/4/6
DI 0.375/0.917/0.889/1/0.066/0.807 0.175/0.329/1.014/1/0.16/0.481 0.292/0.885/0.798/1/0.077/0.795 0.603/0.767/0.911/1/0.037/0.832 16/16/16/16/6/16
HiCExplorer 0.377/0.931/0.917/1/0.075/0.868 0.133/0.271/0.646/1/0.139/0.467 0.311/0.903/0.915/1/0.088/0.857 0.525/0.708/0.693/1/0.039/0.881 15/15/13/16/7/16
HiCseg 0.34/0.889/0.838/1/0.045/0.775 0.178/0.347/1.137/1/0.136/0.558 0.256/0.85/0.726/1/0.053/0.762 0.598/0.772/0.98/1/0.026/0.812 15/16/15/16/6/14
IC-Finder 0.338/0.885/0.747/1/0.097/0.869 0.128/0.255/0.598/1/0.152/0.399 0.275/0.853/0.737/1/0.111/0.85 0.491/0.693/0.626/1/0.052/0.898 14/14/11/16/9/15
Matryoshka 0.331/0.857/0.591/1/0.16/0.748 0.14/0.276/0.506/1/0.203/0.257 0.266/0.819/0.571/1/0.18/0.72 0.509/0.728/0.509/1/0.095/0.804 13/15/10/16/13/11
MrTADFinder 0.183/0.592/0.179/1/0.231/0.47 0.081/0.135/0.237/0.286/0.097/0.114 0.143/0.532/0.134/0.857/0.23/0.428 0.325/0.492/0.26/0.857/0.141/0.563 4/4/4/12/13/4
OnTAD 0.36/0.925/0.758/1/0.07/0.875 0.146/0.294/0.643/1/0.146/0.496 0.291/0.894/0.732/1/0.082/0.863 0.487/0.734/0.539/1/0.037/0.897 14/15/10/16/7/16
SpectralTAD 0.294/0.804/0.743/1/0.093/0.879 0.111/0.213/0.587/1/0.131/0.384 0.237/0.767/0.714/1/0.106/0.856 0.422/0.615/0.608/1/0.049/0.914 10/10/11/16/8/15
TADbit 0.369/0.902/0.872/1/0.062/0.825 0.17/0.314/0.951/1/0.149/0.495 0.287/0.869/0.788/1/0.073/0.812 0.587/0.758/0.859/1/0.035/0.848 16/16/15/16/6/16
TADtree 0.28/0.842/0.412/1/0.22/0.72 0.117/0.242/0.348/1/0.196/0.189 0.227/0.802/0.4/1/0.243/0.683 0.416/0.681/0.316/1/0.128/0.795 10/13/7/16/16/10
TopDom 0.386/0.916/0.883/1/0.094/0.873 0.141/0.28/0.605/1/0.163/0.417 0.316/0.891/0.878/1/0.11/0.855 0.541/0.73/0.683/1/0.051/0.901 15/15/13/16/9/15
  1. For each regulatory element, values from left to right represent (1) Mean peak near inferred TAD boundaries, (2) Inferred TAD boundaries boundary tagged ratio, (3) Fold change (\(\log _2\)) between bilateral regions and TAD boundary regions, (4) p value (\(\le 0.05\)) of mean peak near inferred TAD boundaries in bilateral regions, (5) JI between functional regulatory elements and TAD boundaries using the number of TAD boundaries as numerator, and (6) JI between functional regulatory elements and TAD boundaries using number of regulatory elements as numerator, respectively. The final column is sum of each caller’s ranking in terms of the whole set of functional regulatory elements. Bold numbers show the leading result for every column