Construction of an integrated functional linkage network (FLN) with applications in prioritizing candidate disease genes and quantifying the disease-disease associations. Functional associations between genes are retrieved from diverse data sources (Table 1). These functional associations are then integrated into one single FLN using a naïve Bayes classifier, in which the nodes represent individual genes and the weighted edges represent the degree of their overall functional association upon combining all contributing data sources. Green arrows represent the two steps of using of the FLN for candidate disease gene prioritization: step 1, given a particular disease (Disease I), label genes known to be associated with this disease as seeds (pink colored nodes); step 2, prioritize all other genes in terms of their association with the disease based on the sum of the weights of their network links to the seed genes. The purple arrows represent the two steps of using the FLN to quantify the disease-disease associations: step 1, label genes known to be associated with different diseases with different colors (gene K is labeled with two colors since it is associated with two diseases); step 2, quantify the associations between any two diseases based on the degree of association between the two corresponding disease gene sets within the FLN.
Linghu et al. Genome Biology 2009 10:R91 doi:10.1186/gb-2009-10-9-r91