Figure 2
From: Enriching for direct regulatory targets in perturbed gene-expression profiles
Edge-removal criteria. (a) Pseudocode of the algorithm including positive and negative regulation. Acc(i) and Adj(i) indicate the accessibility and adjacency lists for gene i, respectively, and Acc(i,j) indicates the value (+1 or -1) of the edge from i to j. (b) The original algorithm will pare away any edge connecting two nodes that already have a pathway between them. (c) Algorithm taking positive and negative regulation into account will only pare away an edge if its sign is equal to the product of the signs of the remaining edges in the pathway.