The graph compactness (C p ) is a cluster validity index that indicates how 'compact' (or homogeneous) the clusters are, based on their intra-connectivity characteristics.
We find that the addition of a charged group produces networks with depleted intra-connectivity, which translates to a mechanically weaker and more deformable network.
Additionally, for both conditions, the results suggest that increasing density of connectivity links (intra-connectivity links or inter-connectivity links) can increase the robustness of the system, while the interdependency links decrease its robustness.
Taking into account GO term and intra-connectivity, the major functional modules contain an enrichment of cell cycle, extracellular matrix, glycolysis/fast twitch muscle subunits, slow twitch muscle subunits, nuclear-encoded mitochondrial and mitochondrially-encoded mitochondrial genes.
However, we observed a very tight intra-connectivity within the groups of nervous tissues, blood cells, testis tissues, and muscles, suggesting that the identity of these anatomical structures is determined by the differential expression of many genes.
The cluster detection algorithm used, MCODE, relies on a major parameter called the "node score cutoff", which influences size of the detected clusters and their intra-connectivity.
As the Blue module is a rather large module, we looked into some intra-modular characteristics: the intra-modular connectivity and the Gene-Trait correlations with the OI.
Genes in the module were retained when their intra-modular connectivity was >0.6, and when their intra-modular connectivity with other modules was >0.6.
Thus, genes in selected modules were only retained in the selected modules if: (i) their intra-modular connectivity was > 0.6; (ii) their intra-modular connectivity with other modules was < 0.6, and; (iii) the absolute correlation of the gene expression with the EBV status was > 0.5.
Genes in the differentially co-expressed modules were retained only if: (i) the intra-modular connectivity was > 0.6, and; (ii) the intra-modular connectivity with other modules was < 0.6.
Genes in the differentially co-expressed modules were retained in the selected modules only if: (i) their intra-modular connectivity was > 0.6, and; (ii) their intra-modular connectivity with other modules was < 0.6.
