Figure 1

A family-oriented overview of the input PPIs. A 4-way Venn diagram illustrating the overlap of PPI evidence between four of the considered seven species: human, yeast, fly and worm. Each cell in the diagram is labeled with the number of pairs of protein families for which members interact in the corresponding species. For example, there are 742 pairs of protein families such that in both yeast and human there exists at least one interaction between members of the two families and no such interactions exist for fly and worm. Only about 0.5% (42514 of 8280415) of possible family pairs we consider have any evidence for interaction in any of the four species. Of these only 0.1% (45 of 42514) have evidence in all four species, which seems small, given that all considered families are evolutionarily conserved. However, the size of the overlap presumably corresponds to the fraction of the interactomes sampled experimentally, rather than to the actual level of conservation. For example, while there is a significant size difference between the overlap of the relatively best sampled yeast and human interactomes (742+175+45+42 = 1004 family pairs) and the overlap between yeast and worm interactomes (23+45+42+78 = 188 family pairs), the fraction of family pairs with PPI evidence from human and worm overlapping with such pairs in yeast is of the same magnitude (8% and 9%, respectively). It is highly probable that many of the homologous interactions in yeast and human have, yet unidentified, counterparts in worm and similarly in the other species. CAPPI uses phylogenetic information and probabilistic modeling to identify the most probable interactions in each species given the joint evidence from all input datasets and considering their reliability.