Combining real connectivity with synthetic expression. The network connectivity for each of the three GO networks: Biological Process, Cellular Component and Molecular Function were combined with synthetic expression data. In each case, the 300 most down-regulated genes which were defined using the real yeast diauxic shift data were allocated expression from a N(2,1) distribution and the remainder of the genes were given expression from a N(0,1) distribution. Again we measure the AUC for the ranking. In all cases an improvement over expression ranking is observed for lower values of d although for the Molecular Function network this change is slight. Applying the algorithm to the Cellular Component network achieves the highest overall AUC. The results begin to decrease in quality for d > 0.55, except for the Cellular Component network where the results decrease for d ≈ 0.65.
Morrison et al. BMC Bioinformatics 2005 6:233 doi:10.1186/1471-2105-6-233