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 |