Fig. 3

Distribution of the number of cycles in all networks and in networks with an excess of squares. a Distribution of the number of elementary squares, as well as elementary hexagons and octagons (inset) in all protein-based networks. b Distribution of the number of squares in 1,000 randomized networks derived from the giant component of the HLA-B network, whose number of squares (21) is indicated by a red arrow. c Number of squares (black circles) in the largest components of the haplotype networks of 42 genes with significantly more squares than expected by chance alone, together with the mean number of squares (blue circles) found in 1,000 randomly generated networks for each gene. Shaded areas depict the maximum and minimum number of squares in the randomized networks. Note the logarithmic scale on the vertical axis.