Detecting phenotype-driven transitions in regulatory network structure

Methods to compare networks and find changes in modular structure. “Community comparison” identifies communities separately in each network and looks for nodes that change their community membership. “Edge subtraction” finds communities by subtracting the networks and finding communities in the resulting differential edges (red arrows). ALPACA looks for groups of genes that are more interconnected in the perturbed network than expected given the community structure of the baseline network. Flowchart shows the major steps in the implementation of ALPAC