A predicted protein interactome for rice
1 Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
2 Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
3 Department of Automation, Shanghai Jiao Tong University, No.800 Dongchuan Road, Shanghai, 200240, China
4 Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
5 Department of Plant Biology, Southern Illinois University Carbondale, 1125 Lincoln Ave., Life Science II, Carbondale, IL 62901-6509, USA
Rice 2012, 5:15 doi:10.1186/1939-8433-5-15Published: 2 July 2012
Protein-protein interactions (PPIs) create the steps in signaling and regulatory networks central to most fundamental biological processes. It is possible to predict these interactions by making use of experimentally determined orthologous interactions in other species.
In this study, prediction of PPIs in rice was carried out by the interolog method of mapping deduced orthologous genes to protein interactions supported by experimental evidence from reference organisms. We predicted 37112 interactions for 4567 rice proteins, including 1671 predicted self interactions (homo-interactions) and 35441 predicted interactions between different proteins (hetero-interactions). These matched 168 of 675 experimentally-determined interactions in rice. Interacting proteins were significantly more co-expressed than expected by chance, which is typical of experimentally-determined interactomes. The rice interacting proteins were divided topologically into 981 free ends (proteins with single interactions), 499 pipes (proteins with two interactions) and 3087 hubs of different sizes ranging from three to more than 100 interactions.
This predicted rice interactome extends known pathways and improves functional annotation of unknown rice proteins and networks in rice, and is easily explored with software tools presented here.