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

Sefer, Emre

doi:10.1186/s12859-022-04674-2

BMC Bioinformatics

Table 4 The inferred TAD boundaries boundary tagged ratio for 10 functional elements over normalized interaction dataset from 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	0.695	0.311	0.351	0.630	0.156	0.860	0.570	0.998	0.530	0.501	18
Arrowhead	0.910	0.442	0.512	0.747	0.229	0.911	0.832	0.999	0.796	0.647	32
CaTCH	0.484	0.303	0.341	0.398	0.166	0.488	0.448	0.569	0.429	0.417	9
Constrained HAC	0.910	0.469	0.550	0.737	0.248	0.887	0.856	0.987	0.826	0.672	34
CHDF	0.733	0.338	0.383	0.647	0.161	0.849	0.624	0.978	0.590	0.513	20
ClusterTAD	0.779	0.471	0.533	0.689	0.243	0.807	0.712	0.981	0.691	0.679	29
deDoc	0.858	0.435	0.499	0.724	0.218	0.876	0.788	0.996	0.760	0.636	32
DI	0.920	0.530	0.598	0.747	0.289	0.909	0.858	0.996	0.828	0.733	36
EAST	0.821	0.404	0.476	0.707	0.200	0.880	0.728	0.992	0.694	0.610	27
GMAP	0.848	0.416	0.482	0.699	0.214	0.883	0.740	0.996	0.704	0.628	30
GRiNCH	0.849	0.419	0.485	0.702	0.216	0.884	0.745	0.998	0.705	0.626	30
HiCExplorer	0.942	0.490	0.559	0.770	0.257	0.906	0.894	0.997	0.870	0.698	36
HiCKey	0.944	0.492	0.561	0.768	0.259	0.908	0.894	0.997	0.870	0.699	36
HiCseg	0.872	0.505	0.576	0.706	0.278	0.870	0.804	0.988	0.771	0.705	36
IC-Finder	0.890	0.476	0.535	0.739	0.239	0.902	0.819	0.999	0.789	0.669	35
InsulationScore	0.828	0.430	0.485	0.681	0.208	0.881	0.719	0.971	0.678	0.640	29
Matryoshka	0.740	0.358	0.403	0.639	0.185	0.873	0.628	0.997	0.590	0.544	22
MrTADFinder	0.702	0.294	0.348	0.704	0.130	0.857	0.567	0.998	0.529	0.508	18
MSTD	0.853	0.380	0.450	0.689	0.194	0.872	0.766	0.991	0.726	0.609	27
OnTAD	0.926	0.507	0.577	0.758	0.263	0.910	0.867	0.998	0.841	0.712	36
Spectral	0.665	0.305	0.361	0.649	0.131	0.786	0.548	0.920	0.514	0.477	15
SpectralTAD	0.834	0.399	0.464	0.703	0.200	0.881	0.754	0.998	0.721	0.601	27
TADBD	0.864	0.436	0.499	0.712	0.216	0.901	0.770	0.999	0.737	0.630	30
TADbit	0.912	0.530	0.596	0.763	0.276	0.916	0.844	0.998	0.814	0.731	36
TADpole	0.807	0.421	0.471	0.717	0.205	0.885	0.704	0.998	0.673	0.604	28
TADtree	0.805	0.419	0.470	0.716	0.204	0.883	0.703	0.998	0.671	0.600	28
TopDom	0.897	0.471	0.534	0.730	0.242	0.881	0.841	0.996	0.817	0.674	34

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

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