Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

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 Brassi...

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Main Authors:	Yang, Jianhua, Osman, Kim, Iqbal, Mudassar, Stekel, Dov J., Luo, Zewei, Armstrong, Susan J., Franklin, F. Chris H.
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537189/

id	pubmed-3537189
recordtype	oai_dc
spelling	pubmed-35371892013-01-04 Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana Yang, Jianhua Osman, Kim Iqbal, Mudassar Stekel, Dov J. Luo, Zewei Armstrong, Susan J. Franklin, F. Chris H. Plant Science 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. Frontiers Media S.A. 2013-01-04 /pmc/articles/PMC3537189/ /pubmed/23293649 http://dx.doi.org/10.3389/fpls.2012.00297 Text en Copyright © 2013 Yang, Osman, Iqbal, Stekel, Luo, Armstrong and Franklin. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Yang, Jianhua Osman, Kim Iqbal, Mudassar Stekel, Dov J. Luo, Zewei Armstrong, Susan J. Franklin, F. Chris H.
spellingShingle	Yang, Jianhua Osman, Kim Iqbal, Mudassar Stekel, Dov J. Luo, Zewei Armstrong, Susan J. Franklin, F. Chris H. Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana
author_facet	Yang, Jianhua Osman, Kim Iqbal, Mudassar Stekel, Dov J. Luo, Zewei Armstrong, Susan J. Franklin, F. Chris H.
author_sort	Yang, Jianhua
title	Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana
title_short	Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana
title_full	Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana
title_fullStr	Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana
title_full_unstemmed	Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana
title_sort	inferring the brassica rapa interactome using protein–protein interaction data from arabidopsis thaliana
description	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.
publisher	Frontiers Media S.A.
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537189/
_version_	1611944629653995520

Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

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