Describing the orthology signal in a PPI network at a functional, complex level

In recent work, stable evolutionary signal induced by orthologous proteins has been observed in a Yeast protein-protein interaction (PPI) network. This finding suggests more connected subgraphs of a PPI network to be potential mediators of evolutionary information. Because protein complexes are also likely to be present in such subgraphs, it is interesting to characterize the bias of the orthology signal on the detection of putative protein complexes. To this aim, we propose a novel methodology for quantifying the functionality of the orthology signal in a PPI network at a protein complex level. The methodology performs a differential analysis between the functions of those complexes detected by clustering a PPI network using only proteins with orthologs in another given species, and the functions of complexes detected using the entire network or sub-networks generated by random sampling of proteins. We applied the proposed methodology to a Yeast PPI network using orthology information from a number of different organisms. The results indicated that the proposed method is capable to isolate functional categories that can be clearly attributed to the presence of an evolutionary (orthology) signal and quantify their distribution at a fine-grained protein level.