In earlier versions of GeneMANIA, we found the co-expression networks added a lot of interactions without adding much predictive power for GO annotation. As such, we restricted the number of co-expression networks included by default to 20. This also reduces the number of network weights (in the default settings), and thereby reduces risks for overfitting these weights for short query lists [see (5) for details]. However, we have recently added an additional filter on co-expression links. Now, every co-expression link has been seen in at least one other network (co-expression or otherwise), otherwise it is filtered out. This change removed ∼50% of our total interactions with limited change in the AUROC of our GO term predictions and a slight increase in area under the precision-recall curve of our predictions (see ALGORITHM AND SOFTWARE EVALUATION for more details).
