Singling out functional similarities in graph databases

A technique to search functional similarities in PPI networks

We describe a method to search for similarities across protein-protein interaction networks of different organisms. The technique core consists in computing a maximum weight matching of bipartite graphs resulting from comparing the neighbourhoods of proteins belonging to different networks. Both quantitative and reliability information are exploited. We tested the method on the networks of S. cerevisiae, D. melanogaster and C. elegans. The experiments showed that the technique is able to detect functional orthologs when the sole sequence similarity does not prove itself sufficient. They also demonstrated the capability of our approach in discovering common biological processes involving unc…

Bi-GRAPPIN: Bipartite graph based protein-protein interaction networks similarity search

Asymmetric Global Alignment of Protein-Protein Interaction Graph Databases