For each of the three tasks we are considering (uncovering complexes, BP functional modules and CC functional modules), we utilize several measures to ascertain (i) how well each cluster maps to a known group and (ii) how well each group maps to a cluster.
To identify biologically meaningful coherent modules, we utilized a multiobjective genetic algorithm to extract MFRMs for each comodule.
In order to infer the hierarchical organization of these modules, we utilized a bootstrap ensemble, from which we estimated an ensemble of networks.
In the proposed method, three modules are applied: A) modification of the moving direction by the localization method, B) re-planning the paths, and C) re-planning the delivery positions, which are applied in the order of A, C, then B because latter half of the re-plan module C is the same as the re-plan module B. For module B, we utilize one of the existing methods [21].
Similarly, we utilize the same module as the planning phase to re-plan the delivery position.
Before making this decision, we utilize the performance estimation module to predict the execution time and cost which are the decision indicators in GAs.
To better assess relationship between individual genes in the Brown module and atherosclerosis, we utilized Network Edge Orienting NEOO), a freely available R package [ 34], to assess the causal relationships between the peak SNP associated with IA lesion size, rs368994, the hepatic expression of genes contained in the Brown module and IA atherosclerosis.
To pave the way for implementation of synthetic regulation modules in mammalian systems we utilized lentiviral transduction of synthetic modules.
To search for enrichments in biological gene ontology (GO) functions linking the Finnish and Mexican TG modules to adipose TG regulation, we utilized the DAVID database [ 16, 17].
In addition, we utilized high thresholds for module construction for further filtering, resulting in a final gene coexpression network comprising 26,030 genes, including 4,070 lncRNAs, which are distributed among 16 gene modules labeled by colors.
