Figure 4

Vertical relationship between levels 4 and 5, and horizontal relationships among modules at levels 4 and 5 in PPI Network. (A) The vertical relationship is visualized by dashed green links, and the horizontal relationships at levels 4 and 5 are shown by the solid blue and solid gray links, respectively. With horizontal relationships at the same level, modules enriched by the same annotation category are linked with thicker and darker lines. In contrast, with vertical relationships between different levels, modules enriched by the same annotation category are often merged into a larger module at a higher level. This suggests that Pyramabs can produce a meaningful abstraction hierarchy from the PPI network that corresponds well to known biological processes. (B) The discovered vertical relationships for the five level-5 modules, indexed by 80-83 and 70, which combined to module 46 at level 4. Note that the p-value (next to dashed line) for module 46 at level 4 is much smaller than that for each of the modules (80-83 and 70) at level 5. This justified the merge of these modules into a higher-level module. (C) There is greater proximity between modules 267 and 91 than between modules 91 and 84 and between 91 and 172, as indicated by the thickness and darkness of the links. By merging modules 267 and 91 into a new module, we noted a drop in p-value by 49.49%. Compared with combining modules 91 and 84 (19.76% drop in p-value) or modules 91 and 172 (3.17% drop in p-value), the greater proximity between modules 267 and 91 in the horizontal relationship correctly demonstrates their greater functional similarity.