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Therefore, these approaches would not be expected to be maximally effective in constructing modules with strong association to biological functions [ 16, 17].
By investigating the evolutionary profiles of the modules and their MPD/MNTD coordinates, we found that most (64%) modules with strong tree-level clustering were dominated by widely conserved genes, and that 11 modules with strong tip-level clustering were dominated by clade-specific genes.
Here, we present an analysis delineating a correlation-based gene expression landscape of breast cancer that identifies modules with strong associations to breast cancer-specific and general tumor biology.
These consistent results show that MTB is a robust method for identifying miRNA-mRNA modules with strong expression relationships despite the fact that gene expression data were not used in defining the MTBs.
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Smaller minimal |r| values indicate more "diffuse" co-expression modules with weaker co-expression relationships, and larger minimal |r| values indicate "tighter" co-expression modules with stronger co-expression relationships.
Optionally, modules with a strong correlation can be merged.
The two modules associated with both factors are the two modules with the strongest competitive regulatory mechanisms in the network.
They are predicted to co-regulate modules with other, stronger regulators, and typically do not regulate modules by themselves.
To address this, we performed MMC analysis on the genes significantly correlated with each gross phenotype (weight, triglycerides, and sugar) at a significance threshold of P = 0.01 (1154, 206, and 565 transcripts respectively, File S3) and identified modules of genes with strong correlation in expression pattern.
Based on an estimation of "traffic" values (Table 1), Module 7 again is shown to be the module with the strongest inter-module mediating capability (median traffic = 264).
The module with the strongest association to physiologically relevant GO categories that also possessed regulatory loci for both tissues was the yellowgreen module in the hippocampus (saddlebrown in striatum).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com