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The WGCNA package includes statistical tests to analyze module preservation across different datasets [ 76].
After registration, the agreement/disagreement of these two virtual models was analyzed (Analyze module in 3-matic, Materialise, Belgium).
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A significant validation criterion of our approach was to analyze modules in terms of protein complexes they contain.
The authors used a computational approach to analyze modules of genes with a common regulation that are affected by specific DNA polymorphisms.
Module level analysis has been extensively applied in genome wide level analysis, exploring the organization of biological systems from identifying modules to reconstructing module networks and analyzing module dynamics.
While analyzing modules against 100 random samples from the merged dataset, we found that module preservation (mean Z-summary scores) ranged from 6.86 to 30.27 (Fig. 3b).
TFBS enrichment analysis was conducted by scanning the promoter sequence of the genes in the analyzed modules for enrichment of known transcription factor binding motifs using the Clover algorithm [ 52].
Group-wise effects on Ki-67 staining intensity for genes in the two proliferation modules were analyzed per module by comparing the mean module Ki-67 intensity to a random intensity distribution based on 10,000 sampled gene groups of the same size as the assayed module.
The independence of the functional requirements is used to analyze the module function of the actuator in the functional analysis.
The system consists of a user interactive interface, a product model-processing module, a function execution module, a data recording and process analyzing module.
The lowest voltage (60 V) was applied to prevent complex decomposition and to ensure efficient transport of the generated ions to the analyzing module.
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