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Figure 3 | BMC Bioinformatics

Figure 3

From: Phylogenetically informed logic relationships improve detection of biological network organization

Figure 3

Gene triplets reveal biological networks at different levels and key genes in those networks. A: The basic network structures for logic types 1 (ca b), 3 (ca b), 5 (ca ~b), and 7 (ca b); black dots represent chemical compounds. Type 5 means protein b may inhibit enzyme a or c. These structures can be applied locally to infer protein function, or on a larger scale to reveal protein network organization. B: An example illustrating the power of logic triplets to deduce the network of KDO2-lipidA synthesis [20]; dashed line represents a series of sequential steps catalyzed by different enzymes on different intermediate compounds. The pathway consists of three parts: i) CMP-KDO biosynthesis I in red; ii) lipid IVA biosynthesis in green; and iii) KDO transfer to lipid IVA I in blue. The listed logic triplets convincingly disclose the structure of the whole pathway, the order of enzymes, and even key proteins (in bold font). C: Logic triplets also reveal the interaction among different pathways in the whole cellular network. The upper diagram indicates that RNA-binding protein hfq regulates gene expression and protein secretion. The lower diagram illustrates the interaction among the major pathways in a cell. Numbers denote the type of logic relationships, and arrows point to the c genes in logic triplets.

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