Sentence examples for cooperative modules from inspiring English sources
These identified modules were then used as query modules (Figure 1c, A1; Figure 1e, A1) to search for cooperative modules to form a directed network where all edges ran from the Query nodes to the Cooperative nodes; (2) Identification of cooperative modules and creation of Disease-specific inter-module cooperation network.
Cooperative modules were identified from prognosis data, which comprised microarray gene expression data generated from cancer patients and a prognosis that was classified as either good outcome (longer survival time) or bad outcome (shorter survival time).
To visualize the distinctness of the cooperative modules in terms of functional enrichment, we created heat maps of the significances (see Figure 4).
However, CTFPs exhibited a noticeable correlation (ρ = 0.434 for CTFPs predicted by method N, ρ = 0.575 for CTFPs predicted by method B, ρ = 0.5 for CTFPs predicted by method T, ρ = 0.492 for CTFPs predicted by method C, Spearman test), suggesting a tendency for CTFPs to form higher-order cooperative modules controlling the expression of genes with similar function(s).
Furthermore, some TF pairs considered as false positives by one method are considered bona fide cooperative TF pairs in other, for instance YNL216W (Rap1) – YIR018W (Yap5), considered as a potential false positive pair by method C (due to lack of experimental support) and accepted by method N as a part of the same cooperative module.
Nonetheless, the researchers claim that there is no statistically significant difference between the effects of individual and cooperative instructional modules regarding simulations.
Molecular COmplex DEtection algorithm (MCODE) [ 12] revealed 12 Cooperative MiRNA Modules (CMM) (Table 3).
We found that the majority of them are well known cooperative TF modules.
Using MCODE on CMN composed of miRNAs up-regulating target genes, 17 cooperative miRNA modules were found (Table 1).
Now one can extract cooperative miRNA modules (CMMs) by applying subnetwork detection algorithms and then characterize and evaluate them in terms of biological relevance.
In this paper, we have developed graph-based approaches to address the problem of finding cooperative TF modules at two levels.
