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 () from mouse ESCs at the 1kb 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 |
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 () between bilateral regions and TAD boundary regions, (4) p value () 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