Identifying protein function and functional links based on large-scale co-occurrence patterns.

We demonstrate that Cliquely can successfully identify known networks from various pathways, including nitrogen fixation, glycolysis, methanogenesis, mevalonate and ribosome proteins. Identifying the virulence-associated type III secretion system (T3SS) network, Cliquely also added 13 previously uncharacterized novel proteins to the T3SS network, demonstrating the strength of this approach. Cliquely is freely available and open source. Users can employ the tool to explore co-occurrence networks using a protein of interest and a customizable level of stringency, either for the entire dataset or for a one of the three domains-Archaea, Bacteria, or Eukarya.