title: FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.
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.
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Colin
authors.identifier: http://orcid.org/0000-0002-5993-0953
authors.initials: C
authors.lastname: Ruprecht
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Amelie
authors.identifier: http://orcid.org/0000-0002-6380-0203
authors.initials: A
authors.lastname: Mendrinna
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Takayuki
authors.initials: T
authors.lastname: Tohge
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Arun
authors.identifier: http://orcid.org/0000-0003-1703-0137
authors.initials: A
authors.lastname: Sampathkumar
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Sebastian
authors.initials: S
authors.lastname: Klie
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Zoran
authors.identifier: http://orcid.org/0000-0003-2671-6763
authors.initials: Z
authors.lastname: Nikoloski
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.).
authors.forename: Staffan
authors.identifier: http://orcid.org/0000-0002-6377-5132
authors.initials: S
authors.lastname: Persson
authors.affiliation: Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.) mutwil@mpimp-golm.mpg.de.
authors.forename: Marek
authors.identifier: http://orcid.org/0000-0002-7848-0126
authors.initials: M
authors.lastname: Mutwil
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055442:Metabolome / Q000235:genetics; D008957:Models, Genetic; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D011058:Pollen / Q000235:genetics / Q000378:metabolism; D053205:Pollen Tube / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D013045:Species Specificity; D014026:Nicotiana / Q000235:genetics / Q000378:metabolism