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Our results show that a robust module network analysis of expression data can provide novel insights of miRNA function in important cellular processes.
Taken together, our results show that novel insights can be gained from a robust module network analysis of miRNA and mRNA expression data and support the view that at least some miRNAs have key regulatory roles in important cellular processes.
With the ability to include directionality, the application of methods for module network analysis using improved PSs instead of genes [45] holds the promise to unravel the hierarchical structure in the control of the cellular pathways and reconstruct the modular structure determining changes in a transcriptional profile.
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In addition to the two main modules, network analysis also identified eight additional modules.
With some modules having large sizes, dimension reduction is needed when conducting module-based network analysis.
A module-based network analysis approach was proposed to highlight the anti-inflammatory mechanisms of curcumin.
Here we confirm by mutation the inputs into the blimp1 cis-regulatory module predicted by network analysis.
All of these alterations, with the exception of CCND1, which did not meet our frequency threshold, are also clustered together within the RB1 module identified by network analysis (Figure 3A).
Second, the two largest modules identified by network analysis correspond very closely to the three critical signaling pathways identified in the original TCGA pathway analysis.
The HIV-related network modules revealed by network analysis using DEPs correspond with the results of some earlier studies.
The HIV-related network modules revealed by network analysis using DEPs correspond with the results of some earlier studies (see Discussion for detailed explanation).
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