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FamNet: A framework to identify multiplied modules driving pathway diversification in plants

Ruprecht, Colin and Mendrinna, Amelie and Tohge, Takayuki and Sampathkumar, Arun and Klie, Sebastian and Fernie, Alisdair R. and Nikoloski, Zoran and Persson, Staffan and Mutwil, Marek (2016) FamNet: A framework to identify multiplied modules driving pathway diversification in plants. Plant Physiology, 170 (3). pp. 1878-1894. ISSN 0032-0889. PMCID PMC4775111. http://resolver.caltech.edu/CaltechAUTHORS:20160119-154624274

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Abstract

Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene co-expression networks have indicated that not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one third of the genes of a plant's genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in co-expression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen and root specific cell wall modules that multiplied to confer tip-growth in pollen tubes and root hairs, respectively. We, furthermore, identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco tissues. The interactive platform, referred to as FamNet is available at http://www.gene2function.de/famnet.html.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1104/pp.15.01281DOIArticle
http://www.plantphysiol.org/content/170/3/1878PublisherArticle
http://www.plantphysiol.org/content/170/3/1878/suppl/DC1PublisherSupplemental Data
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775111/PubMed CentralArticle
ORCID:
AuthorORCID
Ruprecht, Colin0000-0002-5993-0953
Mendrinna, Amelie0000-0002-6380-0203
Sampathkumar, Arun0000-0003-1703-0137
Nikoloski, Zoran0000-0003-2671-6763
Persson, Staffan0000-0002-6377-5132
Mutwil, Marek0000-0002-7848-0126
Additional Information:© 2016 by the American Society of Plant Biologists. Received August 14, 2015. Accepted January 7, 2016. Published January 11, 2016. This work was supported by the Max-Planck Gesellschaft (CR, AM, TT, ARF, SK, ARF, ZN, MM), R@MAP grant as part of his Professorship at University of Melbourne (SP), the European Commission's Directorate General for Research within the 7th Framework Program (FP7/2007-2013) under grant agreement 270089 (MULTIBIOPRO; CR, TT, ARF and SP) and ERA-CAPS grant EVOREPRO (MM). M.M. and S.P. conceived the project, C.R. and A.M. performed the knock-out experiments, T.T. and A.R. performed the metabolomic analysis, S.K., Z.N. and M.M. conceived the bioinformatical analyses, M.M. performed the bioinformatical analyses, M.M., S.P., A.S. and C.R. wrote the article with help from all authors.
Funders:
Funding AgencyGrant Number
Max-Planck Gesellschaft UNSPECIFIED
University of MelbourneUNSPECIFIED
European Research Council (ERC)270089
ERA-CAPSEVOREPRO
PubMed Central ID:PMC4775111
Record Number:CaltechAUTHORS:20160119-154624274
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160119-154624274
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:63780
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:20 Jan 2016 20:46
Last Modified:18 Jul 2017 20:04

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