Topological structure analysis of chromatin interaction networks

BMC Bioinformatics

Table 2 Dependence of a number of connected components, their maximal and average sizes, and edge density from similarity threshold used to construct ’CC graph’

Similarity threshold	Number of components	Max size	Average size	Average density
0.00	48	279	63.2	0.740
0.05	65	223	49.6	0.781
0.10	72	223	46.5	0.785
0.15	85	183	42.0	0.775
0.20	98	183	38.3	0.787
0.25	110	152	34.7	0.782
0.30	128	114	31.6	0.752
0.35	151	107	27.2	0.727
0.40	183	107	22.8	0.713
0.45	220	102	21.4	0.686
0.50	280	100	18.4	0.688
0.55	344	100	16.4	0.680
0.60	450	71	14.9	0.680
0.65	580	70	14.1	0.669
0.70	732	64	12.4	0.641
0.75	959	64	9.9	0.656
0.80	1212	63	8.8	0.653
0.85	1484	55	8.0	0.663
0.90	1789	41	6.7	0.706
0.95	2072	16	5.8	0.748

In ’CC graph’ components represented by vertices are connected by edges if their similarity exceeds the threshold value. The data are given for chromosome 6 but are similar for other chromosomes. The minimal component size is 1 even for similarity threshold 0. Edge density of components with n vertices and m edges is defined as 2m/n(n−1) and shows how close these components are to complete graphs. Average component sizes and average densities are computed taking into account only components with more 4 or more vertices

ISSN: 1471-2105