IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1247-1258. doi: 10.1109/TCBB.2015.2476809. Epub 2015 Sep 25.


Proteins carry out their function in a cell through interactions with other proteins. A large scale protein-protein interaction (PPI) network of an organism provides static yet an essential structure of interactions, which is valuable clue for understanding the functions of proteins and pathways. PPIs are determined primarily by experimental methods; however, computational PPI prediction methods can supplement or verify PPIs identified by experiment. Here, we developed a novel scoring method for predicting PPIs from Gene Ontology (GO) annotations of proteins. Unlike existing methods that consider functional similarity as an indication of interaction between proteins, the new score, named the protein-protein Interaction Association Score (IAS), was computed from GO term associations of known interacting protein pairs in 49 organisms. IAS was evaluated on PPI data of six organisms and found to outperform existing GO term-based scoring methods. Moreover, consensus scoring methods that combine different scores further improved performance of PPI prediction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Fungi / genetics
  • Gene Ontology*
  • Humans
  • Plants / genetics
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps* / genetics
  • Protein Interaction Maps* / physiology
  • Proteins / genetics
  • Proteins / metabolism
  • Proteins / physiology
  • Systems Biology / methods*


  • Proteins