Figure 3

Hierarchical organization of domain bigram network in H.sapiens: a case study. Using a topological overlap matrix [23], domain bigram network in H.sapiens is divided into 123 modules after average-linkage hierarchical clustering and thresholding the clustergram at 0.95. A. the largest connectivity component of domain bigram network is plotted, where each module is suppressed to a node. The node circled with red color is selected as an example to illustrate the hierarchical organization of the modules. B. The node selected in A can be divided into four modules (2, 55, 57, 74; node size indicating the abundance of domain types within the node, or module) when the clustergram threshold is set to 0.90. C. When the clustergram threshold is set to 0.7, a module is further subdivided into several smaller submodules. D. The organization of the modules when setting threshold to 0.5. E. When the threshold is set to 0.3, most modules split into groups that consist of no more than three domains (SCOP annotations). The "parent" module of a sub-module is represented by a color-coded underlying "plate" and the color code of a module is consistent across all panels.