Procedure for calculating conserved co-expression scores. The procedure is illustrated using an example involving KOGs KOG0011 and KOG3438 between human and fly. KOG0011 contains two genes in each species (RAD23A, RAD23B and FBgn0026777, FBgn0039147 in human and fly respectively) while KOG3438 contains one in human (CKS1B) and two in fly (FBgn0010314 and FBgn0037613). For each species a KOG0011-KOG3438 co-expression (thick purple and green arrows) correlation is calculated by taking the mean of all gene-gene combinations (thin black arrows) for the two KOGs. The mean of these species-specific KOG-pair correlations (thick vertical orange arrow) is taken to represent the final multispecies KOG0011-KOG3438 co-expression correlation. This co-expression value is used for all relevant gene-pairs as their KOG-based co-expression score. If co-expression is conserved in both species then this value will be high, if it is high in only one species it will be intermediate, and if it is low in both it will be low.