A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data

Oluwadare, Oluwatosin; Zhang, Yuxiang; Cheng, Jianlin

doi:10.1186/s12864-018-4546-8

Table 7 A comparison of the accuracy spread of the different methods on real Hi-C datasets

From: A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data

	Spearman Correlation
Chromosome	3DMax		3DMax1	MOGEN	ChromSDE	Shrec3D	MCMC5C	LorDG
1	0.8088		0.8062	0.7662	0.7845	0.2951	0.463	0.7101
2	0.8149		0.8126	0.7526	0.7245	0.4482	0.4143	0.7275
3	0.8306		0.828	0.8044	0.814	0.4827	0.1564	0.7459
4	0.8736		0.8715	0.8245	0.8636	0.8203	0.3595	0.8607
5	0.8653		0.8631	0.8266	0.8551	0.7762	0.3813	0.8317
6	0.848		0.845	0.8104	0.8303	0.7465	0.4078	0.8002
7	0.831		0.8278	0.7925	0.8144	0.4087	0.5402	0.7536
8	0.8701		0.8675	0.8236	0.857	0.8152	0.5584	0.8317
9	0.851		0.846	0.7339	0.8184	0.421	0.5584	0.2972
10	0.854		0.8505	0.8129	0.8392	0.6561	0.4967	0.7759
11	0.8433		0.8398	0.8003	0.823	0.6936	0.5559	0.7896
12	0.8558		0.8544	0.8259	0.8413	0.7332	0.3907	0.803
13	0.8584		0.8537	0.8242	0.8381	0.6917	0.4437	0.8007
14	0.8799		0.8754	0.8425	0.8605	0.7123	0.7065	0.7879
15	0.8592		0.8488	0.8255	0.8346	0.6432	0.5246	0.7725
16	0.8466		0.8397	0.7854	0.8188	0.6621	0.6208	0.7345
17	0.837		0.8298	0.8127	0.8083	0.6732	0.557	0.719
18	0.8537		0.8475	0.8139	0.8185	0.3717	0.6197	0.7492
19	0.8668		0.8579	0.8077	0.8397	0.73	0.5362	0.8152
20	0.8392		0.869	0.8146	0.8527	0.6291	0.6361	0.7779
21	0.9017		0.8925	0.8421	0.8704	0.7831	0.841	0.8532
22	0.866		0.8542	0.7977	0.8264	0.1065	0.6554	0.5639
	Pearson Correlation
Chromosome	3DMax		3DMax1	MOGEN	ChromSDE	Shrec3D	MCMC5C	LorDG
1	0.7611		0.7491	0.7697	0.2352	0.2125	0.3497	0.2922
2	0.7511		0.7401	0.7544	0.0042	0.3154	0.314	0.3187
3	0.7603		0.7532	0.7938	0.7238	0.3539	0.1368	0.5597
4	0.7813		0.7691	0.7739	0.8016	0.5922	0.2758	0.6675
5	0.779		0.7661	0.8021	0.7215	0.5732	0.2673	0.6845
6	0.7834		0.7709	0.7883	0.7422	0.5361	0.2705	0.5945
7	0.7471		0.7334	0.7549	0.4693	0.2961	0.405	0.3044
8	0.7994		0.794	0.7988	0.7533	0.5895	0.4138	0.6126
9	0.8046		0.8063	0.6852	0.3711	0.3253	0.4446	0.017
10	0.7836		0.7793	0.7965	0.6214	0.4614	0.3436	0.6428
11	0.7628		0.7542	0.7852	0.7624	0.4761	0.39	0.6636
12	0.8098		0.7856	0.813	0.7533	0.5106	0.2941	0.6727
13	0.8037		0.7887	0.7989	0.7875	0.4544	0.2824	0.6483
14	0.8411		0.8316	0.8357	0.7928	0.4855	0.518	0.6965
15	0.8137		0.7892	0.8165	0.7948	0.4078	0.3745	0.179
16	0.8075		0.804	0.7845	0.6925	0.4726	0.4489	0.6899
17	0.8069		0.7981	0.8164	0.768	0.4662	0.3793	0.6879
18	0.82		0.8079	0.7931	0.5246	0.2697	0.468	0.1519
19	0.847		0.8356	0.8204	0.7674	0.5972	0.3881	0.7552
20	0.7096		0.8347	0.8049	0.6113	0.3825	0.4039	0.731
21	0.8892		0.8784	0.8561	0.802	0.5	0.5663	0.7509
22	0.8396		0.8181	0.7486	0.7958	−0.067	0.5262	0.0737
	Spearman Correlation Of GM06990 (HINDIII &NCOL) Cell
Chromosome	3DMax_HindIII	3DMax_Ncol	3DMax1_HindIII	3DMax1_Ncol	Shrec3D_HindIII	Shrec3D_Ncol	ChromSDE_HindIII	ChromSDE_Ncol
1	0.8088	0.8432	0.8062	0.8412	0.2951	0.3043	0.7845	0.1085
2	0.8149	0.8387	0.8126	0.8367	0.4482	0.2797	0.7245	0.8228
3	0.8306	0.8447	0.828	0.8425	0.4827	0.403	0.814	0.8271
4	0.8736	0.874	0.8715	0.872	0.8203	0.796	0.8636	0.8624
5	0.8653	0.8836	0.8631	0.8816	0.7762	0.8077	0.8551	0.872
6	0.848	0.8701	0.845	0.8677	0.7465	0.556	0.8303	0.8539
7	0.831	0.8509	0.8278	0.8483	0.4087	0.3147	0.8144	0.3709
8	0.8701	0.8509	0.8675	0.8924	0.8152	0.8559	0.857	0.8832
9	0.851	0.8732	0.846	0.8721	0.421	0.2899	0.8184	0.0239
10	0.854	0.8753	0.8505	0.8723	0.6561	0.4865	0.8392	0.8603
11	0.8433	0.876	0.8398	0.8731	0.6936	0.76	0.823	0.8603
12	0.8558	0.873	0.8544	0.8698	0.7332	0.7819	0.8413	0.8531
13	0.8584	0.8665	0.8537	0.8621	0.6917	0.8064	0.8381	0.8457
14	0.8799	0.9	0.8754	0.8965	0.7123	0.6141	0.8605	0.887
15	0.8592	0.8842	0.8488	0.879	0.6432	0.715	0.8346	0.8707
16	0.8466	0.8975	0.8397	0.8921	0.6621	0.7156	0.8188	0.8856
17	0.837	0.8858	0.8298	0.8473	0.6732	0.6988	0.8083	0.866
18	0.8537	0.8701	0.8475	0.865	0.3717	0.7055	0.8185	0.8407
19	0.8668	0.936	0.8579	0.9324	0.73	0.7613	0.8397	0.925
20	0.8392	0.9133	0.869	0.9037	0.6291	0.7128	0.8527	0.8878
21	0.9017	0.9382	0.8925	0.9274	0.7831	0.873	0.8704	0.8688
22	0.866	0.9414	0.8542	0.9359	0.1065	0.7311	0.8264	0.922

Top: The Spearman Correlation Coefficient of 3DMax, 3DMax1, MOGEN, ChromSDE, ShRec3D, MCMC5C, and LorDG on the normalized contact maps of GM06990_HindIII cell, and the Pearson Correlation Coefficient of 3DMax, 3DMax1, MOGEN, ChromSDE, ShRec3D, MCMC5C, and LorDG on the normalized contact maps of GM06990_HindIII cell. Bottom: The Comparison of dSCC values of 3DMax, 3DMax1, ChromSDE and ShRec3D on the normalized contact maps of GM06990 HindIII and Ncol cell
The values denote the distance Spearman correlation coefficient (dSCC) score in the range [−1,1] or the distance Pearson correlation coefficient score (dPCC) in the range [−1,1]

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ISSN: 1471-2164

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