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FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion 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 Expansion in Plants. Plant Physiology, 170 (3). pp. 1878-1894. ISSN 0032-0889. PMCID PMC4775111. https://resolver.caltech.edu/CaltechAUTHORS:20200422-150959678

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Abstract

Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression 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 coexpression 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. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1104/pp.15.01281DOIArticle
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 American Society of Plant Biologists. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Marek Mutwil (mutwil@mpimp-golm.mpg.de). M.M. and S.P. conceived the project; C.R. and A.M. performed the knockout experiments; T.T. and A.R.F. performed the metabolomic analysis; S.K., Z.N., and M.M. conceived the bioinformatic analyses; M.M. performed the bioinformatic analyses; M.M., S.P., A.S., and C.R. wrote the article with help from all authors. This work was supported by the Max-Planck Gesellschaft (to C.R., A.M., T.T., A.R.F., S.K., Z.N., and M.M.), the University of Melbourne (R@MAP grant to S.P.), the European Commission’s Directorate General for Research within the 7th Framework Program (FP7/2007-2013 grant no. 270089 [MULTIBIOPRO] to C.R., T.T., A.R.F., and S.P.), and ERA-CAPS (grant EVOREPRO to M.M).
Funders:
Funding AgencyGrant Number
Max-Planck-GesellschaftUNSPECIFIED
University of MelbourneUNSPECIFIED
European Research Council (ERC)270089
European Research Area Network for Coordinating Action in Plant Sciences (ERA-CAPS)UNSPECIFIED
Issue or Number:3
PubMed Central ID:PMC4775111
Record Number:CaltechAUTHORS:20200422-150959678
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200422-150959678
Official Citation:FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants Colin Ruprecht, Amelie Mendrinna, Takayuki Tohge, Arun Sampathkumar, Sebastian Klie, Alisdair R. Fernie, Zoran Nikoloski, Staffan Persson, Marek Mutwil Plant Physiology Mar 2016, 170 (3) 1878-1894; DOI: 10.1104/pp.15.01281
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:102732
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:23 Apr 2020 14:03
Last Modified:23 Apr 2020 14:03

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