NeMoFinder: Dissecting genome wide protein-protein interactions with repeated and unique network motifs

Recent works in network analysis have revealed the existence of network motifs in biological networks such as protein-protein interaction (PPI) networks. However, existing motif mining algorithms are not sufficiently scalable to find meso-scale network motifs. Also, there has been little or no work to systematically exploit the extracted network motifs for dissecting the vast interactomes.

We describe an efficient network motif discovery algorithm, NeMoFinder, that can mine meso-scale repeated and unique network motifs in large PPI networks. Using NeMoFinder, we successfully discovered, for the first time, up to size-12 network motifs in a large whole-genome S. cerevisiae (Yeast) PPI network. We also show that such network motifs can be systematically exploited for indexing the reliability of PPI data generated via highly erroneous high-throughput experimental methods.

--by Jin Chen, Wynne Hsu, Mong Li Lee and See-Kiong Ng, SIGKDD, 2006