Fig. 1

Illustration of the IDLP framework. Square nodes represent phenotypes, all pairwise phenotype similarity relationships make up the phenotype similarity network. Circular nodes represent genes, all pairwise gene interactions make up the PPI network. Nodes surrounded by oval are query phenotypes (or genes), Nodes surrounded by triangle are seed genes (or phenotypes). a For a query phenotype p, the corresponding related genes are selected as seed nodes. b By modeling the noises in the PPI network, the interactions between gene nodes have been changed. In order to better explain the situation, we consider two extreme cases here, i.e., edge deletion and edge addition. During the optimization of IDLP, the interaction between gene g and f has been added, the interaction between gene d and e has been removed. The changes of the PPI network result in a high score on gene g, because gene g directly receive score from seed gene f. What’s more, gene d no longer receives scores from gene e, which indirectly results in gene d receives more support from gene e. c For a query gene g, the corresponding related phenotypes are selected as seed nodes. d By modeling the noises in the phenotype network, the similarity scores between phenotypes have been changed. The edge addition between phenotype r and p and edge deletion between phenotype r and t result in a high score on phenotype p