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For example, let us take a look at GS03-BC05, an identified module significantly enriched by our GWAS findings.
The confusion matrix contains the number of overlapped nodes between the prescribed modules and the identified module.
The ModuLand method family, even with its simplest NodeLand influence function calculation method correctly identified the observed split of the gold-standard Zachary karate club network [19], while uncovering a third, previously identified module and several club-members in modular overlaps (Figure S1.7 in the Electronic Supplementary Material S1).
Additional information concerns further pathways, processes, and interactions relevant to the identified module 'chemotaxis'chemotaxis
Another identified module is up-regulated with age and enriched for ' Cytolysis' [Fig. 2C].
Since the size of our identified module was generally less than 100, we defined a module to be preserved if it has a Zsummary (module) >5.
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Across all 25 identified modules, there are 9 and 8 unique GS and BC entities, respectively.
We identified modules of co-expressed genes in Cytoscape 2.5.1 [29] using the organic clustering algorithm.
In our case, network module analysis identifies new candidate driver genes within previously identified p53/RB and PI3K signaling modules, and within newly identified modules in glioblastoma.
The rows of the confusion matrix correspond to the prescribed modules, and the columns correspond to the identified modules.
To see the significance of the identified modules, a popular tool, namely MCODE [46], that is developed to detect modules in a protein interaction network was utilized to identify modules in the pathogenic network.
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