Figure 5

Abstraction pyramid disclosed from metabolic network. (A) Modules denoted by different shapes at each level, with shape sizes representing the relative module sizes. Vertical relationships between two levels are visualized by black, pink, and green dashed lines. Horizontal relationships are shown by solid brown, blue, and gray lines at the 2^nd, 3^rd, and 4^th levels, respectively. (B) Modules 31, 32, and 33 at level 4 were most consistent with "Pyrimidine metabolism," a sub-category of the KEGG PATHWAY "Nucleotide metabolism," with p-values of 2.37E-15, 2.17E-05, and 1.03E-04, respectively. We marked the modules with the red, green, and blue dashed lines on the pyrimidine metabolism map provided in KEGG. Merging modules 31, 32, and 33 into a larger module 15 showed higher within-module consistency with the Pyrimidine metabolism sub-category (p-value = 4.20E-25). Module 15, combined with others, formed a level-2 module 5, which mapped most consistently onto the "Nucleotide metabolism" metabolism pathway category, with a p-value of 2.73E-26. These results demonstrated that the vertical relationships disclosed by Pyramabs could characterize inclusion (or part-of) relationships, e.g. "Pyrimidine metabolism" is a sub-category of "Nucleotide metabolism." (C) Modules 1 and 2 are marked with the blue dashed line and the red dashed line on the purine metabolism map in KEGG. The remaining modules in the horizontal relationship mapped onto different pathway categories. The greatest proximity in the horizontal relationship occurred between modules 1 and 2. This result is consistent with modules 1 and 2 belonging to the same metabolism pathway category, while the others belong to various other categories.