Figure 1.
The workflow of our method in prioritizing disease candidate proteins.
First, cardiomyopathy (DCM, HCM or ARVC)-specific PPINs were constructed, which were composed of seed proteins and their direct neighbors (candidate proteins) from human PPIN. Secondly, two weights (interaction confidence scores and functional similarities) were used to measure each protein interaction. The disease relevance score of each protein was measured by using these weights. Finally, the proteins ranked at top of each candidate list in descending order of disease relevance score were taken as potential disease-related proteins.
Table 1.
Official symbols of seed genes of DCM, HCM and ARVC.
Table 2.
Top 50 candidate proteins from DCM-specific PPIN.
Figure 2.
DCM seed proteins are colored in cyan. Red nodes are proteins which were verified to be DCM-related proteins, and yellow nodes represent proteins which are potential DCM-related proteins.
Figure 3.
DCM pathway and its relevant pathways.
DCM pathway is colored in yellow. Purple nodes are DCM-related pathways, and green nodes are other pathways. Black edges connect pathways which are directly connected to the DCM pathway.
Table 3.
AUC for three subtypes of cardiomyopathies obtained using five different methods.
Figure 4.
The number of proteins related with DCM.
50 potential disease proteins identified either by our developed method (the top left circle), or by Chen’s protein ranking method (the top right circle), and the number of proteins which have been confirmed to be related with DCM in literature were plotted.
Table 4.
AUC for three subtypes of cardiomyopathies obtained using GeneMANIA and ToppGenet.