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

Sefer, Emre

doi:10.1186/s12859-022-04674-2

BMC Bioinformatics

Table 3 Fold-change (\(\log _{2}\)) between bilateral regions (500kb) and TAD boundary segments (1kb) for 10 regulatory functional elements over normalized interaction dataset of 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	0.318	0.307	0.285	− 0.269	0.324	0.191	0.389	0.038	0.383	0.359	17
Arrowhead	0.609	0.391	0.372	− 0.356	0.473	0.220	0.695	0.185	0.646	0.557	27
CaTCH	0.549	0.706	0.731	− 0.659	0.813	0.522	0.568	0.127	0.471	0.813	31
Constrained HAC	0.873	0.527	0.663	− 0.409	0.502	0.358	1.062	0.132	0.999	0.785	33
CHDF	0.481	0.363	0.352	− 0.226	0.309	0.265	0.606	0.036	0.613	0.412	23
ClusterTAD	0.515	0.452	0.495	− 0.474	0.478	0.299	0.598	0.032	0.543	0.577	25
deDoc	0.608	0.314	0.293	− 0.284	0.243	0.183	0.773	0.035	0.745	0.420	20
DI	0.644	0.630	0.616	− 0.438	0.654	0.439	0.714	0.146	0.646	0.721	33
EAST	0.292	0.109	0.233	− 0.077	0.260	0.110	0.372	0.039	0.365	0.062	15
GMAP	0.432	0.291	0.395	− 0.351	0.462	0.292	0.433	0.159	0.381	0.568	24
GRiNCH	0.434	0.294	0.396	− 0.352	0.464	0.295	0.436	0.160	0.382	0.569	24
HiCExplorer	0.696	0.452	0.372	− 0.365	0.332	0.226	0.852	0.082	0.804	0.533	27
HiCKey	0.697	0.454	0.373	− 0.369	0.335	0.228	0.850	0.081	0.802	0.531	27
HiCseg	0.669	0.670	0.699	− 0.405	0.753	0.417	0.689	0.175	0.595	0.810	34
IC-Finder	0.532	0.505	0.424	− 0.286	0.408	0.307	0.635	0.096	0.597	0.521	26
InsulationScore	0.274	0.254	0.201	− 0.329	0.394	0.281	0.339	0.178	0.282	0.328	20
Matryoshka	0.365	0.384	0.347	− 0.295	0.394	0.276	0.460	0.075	0.430	0.410	21
MrTADFinder	0.123	− 0.021	0.004	− 0.136	0.047	− 0.042	0.121	0.004	0.098	0.162	9
MSTD	0.491	0.195	0.197	− 0.489	0.243	0.115	0.568	0.111	0.463	0.499	22
OnTAD	0.603	0.428	0.374	− 0.343	0.418	0.273	0.717	0.117	0.689	0.459	26
Spectral	0.041	0.069	− 0.064	0.010	0.108	− 0.045	0.052	− 0.004	0.045	0.046	9
SpectralTAD	0.544	0.425	0.410	− 0.230	0.361	0.221	0.669	0.057	0.634	0.491	24
TADBD	0.213	0.151	0.139	− 0.124	0.191	0.122	0.248	0.117	0.246	0.163	13
TADbit	0.598	0.591	0.642	− 0.377	0.632	0.424	0.657	0.165	0.572	0.747	33
TADpole	0.325	0.327	0.254	− 0.121	0.298	0.199	0.387	0.079	0.380	0.295	18
TADtree	0.323	0.325	0.256	− 0.124	0.297	0.196	0.385	0.077	0.381	0.293	18
TopDom	0.673	0.445	0.353	− 0.382	0.311	0.237	0.830	0.062	0.793	0.505	27

The final column is sum of each caller’s ranking in terms of the whole set of functional regulatory elements except H3K9me3. Bold numbers show the leading result for every column

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ISSN: 1471-2105

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