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Most drivers/regulators of these microRNA modules are known or predicted targets of the passenger microRNAs.
We first adopt the simulated annealing (SA) technique to maximize the modularity density and evaluate its advantages on a suit of simulated networks where the modules are known.
To evaluate the ability of PMN to reconstruct regulation pathways, we used a test case in which the regulators and the modules are known.
Notably, in the Drosophila wing, the two independently operating Ds/Fj and Fz/Vang signaling modules are known to function along the same proximal-distal axis (Casal et al., 2006; Devenport, 2014).
Since our knowledge about genome-scale gene networks is incomplete and only a few functional modules are known for higher organisms (Rolland et al., 2014), our aim is to quantify associations between the inferred gene networks and known cellular functions and phenotypes, and to assess the significance of these associations.
Despite their large sequence variability, the GH61s show little variation in terms of their modular nature: of the 534 sequences annotated as GH61 in the Pfam database (Pfam ID: PF03443), 409 have no additional modules, whereas 100 have one additional CBM1 module (CBM1 modules are known to predominantly bind cellulose [ 45, 47]).
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Soiling on modules is known to reduce the transmittance of incident rays to solar cell and cause significant output power degradation.
Current docking algorithms have only had limited success rates, even when the structures of isolated modules were known [61].
Interestingly, genes in this module are known to be involved in metabolism and obesity, and include leptin, PPAR-α, and genes involved in the inflammatory response [22].
Moreover, Snz2p and Snz3p, which are part of this module, are known to respond to nutrient limitation [ 108].
Several hub genes in the Blue module are known to be involved in response to stress and vesicle transport.
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