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The modular assignment of the 16 neighbors of the cAMP-dependent kinase family enriched the modular composition by 4, 11, 8, and 6 modules in case of the NodeLand, InfoMap, Louvain and CFinder methods, respectively.
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Moreover, the Moduland-based, different modular assignment strengths of related nodes (such as those of the 3 cAMP-kinase catalytic subunits; Table S1.4 in the Electronic Supplementary Material S1) give a detailed suggestion on the nodes' functional specificity.
Unfortunately, this modular assignment apparently contradicts many biochemical and functional studies.
In the previous modular assignment, the Middle + Tail modules interact with each other and form the upper portion of Mediator, and the Head module is separated and corresponds to the dense domain at the base.
Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base.
89– 91 The second approach, the modular approach, is to guide the assignment of a function to a gene by the collective function of other genes that belong to a given module in which the investigated gene is located.
Since refinement of domain boundaries (step 2) also involves assignment of structural extensions to a domain, this step influenced the sequential arrangement and modular representation of our domains.
Standards for assignment of the "p.g.a".
Assignment of UH5 also allows rapid assignment of UH6.
(B ) Functional assignment of COGs by phylum assignment.
We also compared the modular membership assignment using the normalized mutual information (NMI) (Alexander-Bloch, Lambiotte, et al. 2012).
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