A predicted protein interactome for rice

Abstract

BackgroundProtein-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.ResultsIn 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-15) contains supplementary material, which is available to authorized users.

A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways

“…The distribution of the correlation values is shown in Figure 2 . It can be seen from the distribution correlation values, that a majority of the correlations are skewed to the right (positive correlations) as has been shown in other co-expression analyses, including Arabidopsis and rice (Geisler-Lee et al, 2007; Ho et al, 2012). Further exploration of this network was to determine how similar the distribution was to a randomly generated distribution (see Materials and Methods).…”

Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice

“…For RPNN-predicted interactions (Fig. 2, step 2), computationally predicted protein-protein interactions were obtained from the PRIN database (Gu et al, 2011) and the Rice journal database (Ho et al, 2012).…”

“…For example, Arabidopsis has much more experimental data with regard to cis-binding sites and protein-protein interaction. To fill these gaps in rice network knowledge, we integrated orthology-based Arabidopsis interaction data (Palaniswamy et al, 2006;Yilmaz et al, 2009;Gu et al, 2011;Ho et al, 2012) and searched for functional Arabidopsis cis-binding sites in rice, to identify N-regulatory network modules and biological processes (network biomodules) conserved between dicots and monocots.…”

Role of Cation/Proton Exchangers in Abiotic Stress Signaling and Stress Tolerance in Plants

“…The determination of function of individual plant genes and gene families, such as the CAX genes, as well as interacting gene networks, has been clearly enhanced through the use of functional genomics techniques such as genome-scale transcriptomics (Maathuis et al 2003 ;Bock et al 2006 ;Narsai et al 2010 ;Patel et al 2012 ) and the systematic analysis of whole gene family function such as by gene knockout (O'Malley and Ecker 2010 ;Wang et al 2013 ), cell-specifi c expression (Toufi ghi et al 2005 ), subcellular localisation (Li et al 2006 ;Winter et al 2007 ) and protein interaction (Geisler-Lee et al 2007 ;Lalonde et al 2010 ;Ho et al 2012 ). Furthermore, methods such as ionomics, to determine the genome-wide variation in element concentration upon changes in expression or knockout of each gene (Salt et al 2008 ), are particularly useful for the study of ion transporters.…”