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

Table 1 The determination of the convergence constant (epsilon) values for the 3DMax algorithm

Chromosome	epsilon = 1	epsilon = 0.5	epsilon = 0.1	epsilon = 0.01	epsilon = 0.0001	epsilon = 0.00001
1	0.8087	0.8088	0.8087	0.8087	0.8088	0.8087
2	0.8149	0.8149	0.8149	0.8149	0.8149	0.8149
3	0.8306	0.8306	0.8306	0.8306	0.8306	0.8306
4	0.8716	0.8716	0.8714	0.8663	0.8735	0.8714
5	0.8645	0.8645	0.8645	0.8646	0.8654	0.8645
6	0.8477	0.8479	0.848	0.8478	0.848	0.848
7	0.8302	0.8302	0.83	0.8302	0.831	0.8301
8	0.8701	0.8701	0.8701	0.8702	0.8701	0.8701
9	0.853	0.853	0.8495	0.8521	0.8532	0.8508
10	0.8538	0.8542	0.8541	0.8538	0.8538	0.8538
11	0.8431	0.8431	0.8431	0.8431	0.8433	0.8432
12	0.8576	0.8576	0.8578	0.8577	0.8578	0.8578
13	0.8581	0.8553	0.8582	0.8582	0.8584	0.8582
14	0.8785	0.8796	0.8797	0.8797	0.8797	0.8797
15	0.8593	0.8563	0.8588	0.8595	0.8565	0.8592
16	0.8441	0.8459	0.8458	0.8459	0.8458	0.8458
17	0.8359	0.836	0.8362	0.8362	0.8362	0.8361
18	0.8521	0.8537	0.8536	0.8535	0.8535	0.8534
19	0.8629	0.8669	0.8663	0.8665	0.8665	0.8664
20	0.8853	0.884	0.8842	0.8865	0.8867	0.8867
21	0.9019	0.8995	0.9016	0.9016	0.9017	0.9018
22	0.8657	0.8658	0.8672	0.8658	0.8659	0.8659
Average dSCC	0.8541	0.8541	0.8543	0.8542	0.8546	0.8544

The dSCC value between the input distance matrix and the representative model for chromosome 1 – 22 of the GM06990 cell line using convergence constant (epsilon): 1, 0.5, 0.1, 0.01, 0.0001, and 0.00001 respectively. The average dSCC values across the chromosomes show that the results are highly comparable. The epsilon = 0.0001 has the highest average dSCC score, hence, we set it as the default epsilon value for 3DMax. The bold text represents the highest dSCC value

ISSN: 1471-2164