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The overlapping of modules between PAG and Cortex and between WGCNA- and MCLUST- produced modules was determined by all-against-all pairwise comparisons with a custom perl script.
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The clustering of SI and triglyceride (TG) indicates a significant overlap of modules correlated with these two traits in CA subjects.
We tested for overlap of modules across tissues on a pairwise basis using the hypergeometric test with a Bonferroni multiple-testing correction (α < 0.05).
We only recently found out about a related method called DetMod [ 17] that addresses many important aspects of detecting functional modules, such as automated detection of the number of modules and potential overlap of modules.
Recent experiments revealing the in vivo intracellular signatures of grid cells, the primarily inhibitory recurrent connectivity of grid cells, and the topographic organisation of grid cells within anatomically overlapping modules of multiple spatial scales along the dorsoventral axis of MEC provide strong constraints and challenges to all three classes of models [18 20].
Additionally, only modules CBneg2 (15/50 = 30%) and CBneg3 (14/50 = 28%) showed considerable overlap of module hub genes and dysregulated genes.
We also tested conservation of SI-associated modules between ethnic groups by analyzing overlap of module members and enrichment of modules for common or ethnic-specific SI-associated genes.
However, we have found this kind of overlapping between modules is sometimes caused by the fact that some of its shared members are proteins with multiple functions.
We have used a generative model of relational data to take into account the uncertainty in PPI data when searching for overlapping functional modules of genes.
This is a concrete example of the benefits of overlapping modules, which, in this example, share ESR1 as a member, but reflect different functionalities.
The Moduland method family defines link-based modules and results in pervasively overlapping modules as some of the few most recent approaches [14], [45] published well after our initial studies [39].
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