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Dense interactions means an agreement problem in a network is solved faster compared with a connected but sparse network, thus a large λ2 provides a faster convergence speed than a small λ2.
In addition, we show that, if RCTs are connected at random (figures 4d), or on a shared characteristic basis (figure 4a, 4b), dense interactions do not appear to translate into treatment success as measured in terms of improvement in cancer survival.
Nevertheless, the dense interactions among these genes are revealed by our method.
In the miRNA-TF regulatory network containing the interactions between TF, miRNA and non-TF protein-coding genes (see Methods), 39 modules that have dense interactions were found using MCODE plus [ 25] of the network tool Cytoscape [ 26].
Since the miRNAs in a homo-cluster bind to similar targets, they tend to form a local community of dense interactions associating them with common targets (see the orange circles in Figure 2a).
SEL1 and UBC7 in module 25 are involved in the ER-associated protein degradation pathway, and the dense interactions in the module can be explained by the cross talk between the OLE and ERAD pathways.
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It is known that the oscillatory, yet transient, dynamics of neuronal assemblies emerges from the dense interaction between excitatory and inhibitory sets of neurons, and when modeled, they could produce chaotic oscillations [5], and the flexible switching between multiple chaotic attractors was earlier demonstrated in the olfactory bulb of rabbits [6].
Our analysis uncovered a remarkably dense interaction node centered on genes involved in mitotic progression.
There is a dense interaction between the AML pathway and signature.
This indicates that the expanded PPI network still does not have dense interaction structures around PRDM9.
The main reason for this issue could be that there are no dense interaction structures around PRDM9.
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