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

Sefer, Emre

doi:10.1186/s12859-022-04674-2

BMC Bioinformatics

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

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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