Fig. 1

Prediction of gene-phenotype association using interaction network and signature genes. The hyperlink matrix and dangling matrix (no outgoing edge matrix) were constructed from interaction databases (red box). The weight matrix was constructed using public annotation databases (orange box). The d represented the dumping factor (0.85). The TSPR score represented the gene association for that particular phenotype. For this given TSPR score vector, A and D were signature genes. The seed nodes were selected from the top three ranking TSPR scores. A and D were good seeds because these two genes were signature genes in the input phenotype and ranked among the top three in the TSPR result. Therefore, d is 2 in this figure, meaning the good seed vector is ½. All other cases were given 0. Finally, phenotype-associated genes were selected from those with a high TrustRank score and low Spammass score