Functional conservation vs. ortholog prediction: comparing experimental results with the OrthoMCL ortholog predictions for disease-related families.

In all but one of these experiments, the yeast gene was mutated and the gene from the other organism was tested for the ability to complement the mutant phenotype. In the one exception, the yeast gene DPM1 was expressed in mouse. In the OrthoMCL column, “Yes” indicates that the OrthoMCL algorithm placed the two proteins in the same ortholog family, while “No” indicates it did not. In the Experimental column, “Yes” indicates functional complementation, while “No” indicates none. Thus, when both columns are the same, the OrthoMCL prediction is consistent with the experimental result i.e. in the cases where both are “Yes,” the predicted orthologs are functionally conserved, and when both are “No,” the proteins are not predicted to be orthologs, and they are not functionally conserved.