Matrix of vertex similaritiesΘ(i,i′) (top) and matrix of correlations between the edge weights of verticesiinG and i′inG′(correlation of i’th column ofAandi′’th column ofA′,cor(i,i′), bottom) for the scenario (iii) and network sizeN = 200. The optimal alignment of the two networks aligns the n-th vertex of G to the n-th vertex of G′. Half of the diagonal terms represents truly orthologous vertices with both vertex and topological similarity (highlighted in green). The other 10% of vertices i in G (highlighted in blue) have two possible vertex similar partners in network G′, one of them with a strong topological match (the true ortholog) and the other with no match (the spurious ortholog). Next, there are 20% of vertices with no vertex similarity but strong topological similarity (analogs, highlighted in red). Scattered off-diagonal terms in θ model spurious weak vertex similarities in the data.
Kolář et al. BMC Systems Biology 2012 6:144 doi:10.1186/1752-0509-6-144