Inferring the Brassica rapa interactome using protein-protein interaction data from Arabidopsis thaliana

被引：17

作者：

Yang, Jianhua ^{[1
]}

Osman, Kim ^{[1
]}

Iqbal, Mudassar ^{[2
]}

Stekel, Dov J. ^{[2
]}

Luo, Zewei ^{[1
]}

Armstrong, Susan J. ^{[1
]}

Franklin, F. Chris H. ^{[1
]}

机构：

[1] Univ Birmingham, Birmingham B15 2TT, W Midlands, England

[2] Univ Nottingham, Nottingham NG7 2RD, England

来源：

FRONTIERS IN PLANT SCIENCE | 2013年 / 3卷

基金：

英国生物技术与生命科学研究理事会;

关键词：

Brassica rapa; Arabidopsis thaliana; interactome; protein-protein interaction; domain-domain interaction; meiosis; DOMAIN-DOMAIN INTERACTIONS; INTERACTION NETWORKS; PLANT INTERACTOMES; DATA INTEGRATION; MISMATCH REPAIR; GENE; GENOME; RECOMBINATION; MEIOSIS; IDENTIFICATION;

D O I：

10.3389/fpls.2012.00297

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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.

引用

页数：15

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