Figure 3

The number of CG iterations and computation time of the GeneMANIA algorithm as a function of number of genes. Left axis: the number of conjugate gradient (CG) iterations until convergence as a function of number of genes in the association networks. Right axis: computation time of GeneMANIA as a function of number of genes in the association networks. Experiments were run using ten association networks from the MouseFunc I benchmark data. The final point on the plot used the full mouse gene complement (for which data are available), and the other gene numbers were derived by taking random subsets of the full gene complement. Distribution is over 100 randomly selected Gene Ontology (GO) categories. The maximum number of CG iterations observed in any test was 20 and the maximum computation time was 15 seconds. The quadratic dependence of computation time on gene number is due to the quadratic growth in number of non-zero association links in the networks as a function of gene number (data not shown).