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A thorough comparison shows that MS outperforms the basic MQ in guiding the optimization algorithms to find more meaningful module clusters for software systems.
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Evans and Lambiotte [45] show that meaningful modules can be found in networks by finding modules of links instead of nodes, so that nodes can trivially belong to multiple modules, if its links do.
The biologically meaningful modules present in the main network could easily be discerned by eye once node colour was mapped to GO term, and were additionally verified by the Cytoscape plug-in MCODE (data not shown).
Topological overlap between two genes reflects not only their direct interaction but also their indirect interactions through all the other genes in the network, and previous studies [30], [61][30], [62][28], [60]have shown that topological overlap leads to more cohesive and biologically more meaningful modules [30].
The method is shown to lead to biologically meaningful modules and networks among the modules.
We propose a new computational method to determine the number of biologically meaningful modules.
SpaCEM provides a stand-alone analysis tool to retrieve meaningful modules of biological objects.
The results indicate that biologically meaningful modules are selected and biologically plausible networks between modules are estimated.
To identify biological meaningful modules, we correlated the module eigengenes to the HD stage assignment of the samples [ 27].
In the current framework, the selection of biologically meaningful modules still need certain amount of manual intervention from biology expert.
At the general level, the network needs to be decomposed into several meaningful modules (such as compartments, pathways).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com