Figure 2

Illustration of orthology definitions. Species A and B are compared. Proteins A1 and B1 are each others' closest cross-species homologs and are considered seed orthologs. Other proteins in A and B are inferred to have descended from the same ancestral gene (and thus be inparalogs) if they are closer to the seed orthologs (inside the circles) than the seed orthologs are to each other. If this is not the case (proteins outside the circles), then they are inferred to be outparalogs. Two inparalogs in the same species (any two black circles or squares, respectively) form an inparalog-inparalog (iP) pair. Any cross-species pair of cluster members (any black circle vs any black square) form an ortholog-ortholog (O) pair. For all cluster members, the pair formed with the closest same-species protein outside the cluster (black square and closest white square, black circle and closest white circle) form an ortholog-closest same-species outparalog (oPs) pair. Likewise for all cluster members, the pair formed with the closest cross-species protein outside the cluster (black square and closest white circle, black circle and closest white square) form an ortholog-closest cross-species outparalog (oPx) pair.