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Chunk #18 — Methods — Paraclique formation and network analysis

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Genetic dissection of acute ethanol responsive gene networks in prefrontal cortex: functional and mechanistic implications.
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The relative importance of each node within a paraclique was assessed using network topological measures of connectivity and centrality. Degree of connectivity was equal to number of edges linking a probe-set to other paraclique members, based on the |0.7| edge correlation threshold used to construct the unweighted graphs. Betweenness centrality measures how frequently a node is included in the shortest paths between all pair-wise members of a network. With the edge threshold at |0.7|, Spearman's rank correlations were typically >0.9 between centrality and connectivity. Increasing the edge correlational threshold to |0.9| reduced the connectivity/centrality correspondence to ∼0.6 and greatly increased the centrality for a subset of nodes situated between densely inter-connected subnetworks. We therefore used betweenness centrality scores within unweighted graphs constructed using the more stringent |0.9| edge threshold as a supplemental measure of node importance. Both measures were calculated using the igraph package for R [35].