ArticleFrontiers in plant science2012
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana.
Article in Frontiers in plant science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Article
- Article
- Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus.BMC plant biology · 2020Article
- Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants.Molecular biology and evolution · 2020Article
- Article
- Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs.Frontiers in plant science · 2018Review
- PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions.Database : the journal of biological databases and curation · 2017Article
- Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato (Frontiers in plant science · 2017Article
- Techniques for the Analysis of Protein-Protein Interactions in Vivo.Plant physiology · 2016Review
- PTIR: Predicted Tomato Interactome Resource.Scientific reports · 2016Article
- Understanding Brassicaceae evolution through ancestral genome reconstruction.Genome biology · 2015Article
- The Reference Genome of the Halophytic Plant Eutrema salsugineum.Frontiers in plant science · 2013Article
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7 authors.
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Abstract
Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein-protein interaction (PPI) data are available from the major PPI databases (DBs). It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B. rapa interactome that is based on the A. thaliana PPI data from two resources: (i) A. thaliana PPI data from three major DBs, BioGRID, IntAct, and TAIR. (ii) ortholog-based A. thaliana PPI predictions. Linking between B. rapa and A. thaliana was accomplished in three complementary ways: (i) ortholog predictions, (ii) identification of gene duplication based on synteny and collinearity, and (iii) BLAST sequence similarity search. A complementary approach was also applied, which used known/predicted domain-domain interaction data. Specifically, since the two species are closely related, we used PPI data from A. thaliana to predict interacting domains that might be conserved between the two species. The predicted interactome was investigated for the component that contains known A. thaliana meiotic proteins to demonstrate its usability.
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