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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks

Fig. 3

Overview of the InferA algorithm and its use with FGES. a The pseudo code of algorithm InferA. “All\ij” refers to all the nodes except Aij, “pa(Aij)” refers to the parents of Aij, and “Aijc” represents a child node of the Aij node. “initial_Net” refers to the initial network, which is discussed in the subsection of “construction of initial networks” within the methods section. b The pipeline of InferA-FGES for predicting the causal network among phosphoproteins. Within the three networks shown in the pipeline, P nodes represent protein phosphorylation states; A nodes represent protein activity states; the gray edges are the default edges between each protein’s P node to its A node while the black edges represent the causal relationships among proteins; the black edges in the initial_Net were provided to InferA for inferring the A node values while the black edges in the predicted network outputted by FGES were learned by the pipeline. The unfilled ovals represent A nodes with unknown values while the filled ovals or squares denote nodes with known values

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