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A pathway in KEGG is a set of genes known to function as a module according to the literature.
The higher the weight of a clique, the more likely the TFs in the clique will function as a module.
First, if a set of neurons were to function as a module it should not consist of two (or more) disconnected subsets.
Additionally, Ubp8 and Sgf11 together regulate a subset of genes, and so have been revealed to function as a module in yeast [ 14].
Therefore, as a gene solely expressed in pollen, WRKY34 potentially promotes the expression of FER3, RHD2 and GRP4, which may function as a module to balance the reactive oxygen species metabolism during the process.
We evaluated this assumption looking at two factors: 1) whether members of the cliques are known to function as a module based on literature, and 2) whether the members of the cliques have shown physiological or genetic interactions in previous experiments.
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We have performed electronic transport calculations based on DFT [9, 12] for both structures A and B. These calculations have been carried out with the help of our code ANT.G, which is part of the package ALACANT [9] and implements the non-equilibrium Green's function formalism as a module to the popular code GAUSSIAN09 [12].
However, it is also possible that groups of nodes function together as a module without any obvious topological signature.
One is DNA-binding specificity of combinations of NF-κB heterodimers [ 5], which allows two κB sites function together as a module, which differentially regulates gene activation.
Thus the VPS15 kinase and HEAT regions function as a single module.
Thus, AMPKαSsp2, Tsc1/2, and Rhb1 appear to function as a signaling module upstream of TORC1 under these conditions.
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