FamNet: A framework to identify multiplied modules driving pathway diversification in plants
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.
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).Attached Files
Accepted Version - Plant_Physiol.-2016-Ruprecht-pp.15.01281.pdf
Supplemental Material - 01281Supplementary_Material_Pipeline_to_detect_similar_gene_modules-1.docx
Supplemental Material - PP2015-01281R2_Supplemental_Figure_S1_S10.pdf
Supplemental Material - PP2015-01281R2_Supplemental_Material_1_4_11.xlsx
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Arabidopsis_modulesA.txt
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Barley_modulesB.txt
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Medicago_modulesC.txt
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Poplar_modulesD.txt
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Rice_modulesE.txt
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Soybean_modulesF.txt
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Tobacco_modulesG.txt
Supplemental Material - PP2015-01281R2_Supplemental_Material_3_Wheat_modulesH.txt
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Additional details
- PMCID
- PMC4775111
- Eprint ID
- 63780
- Resolver ID
- CaltechAUTHORS:20160119-154624274
- Max-Planck Gesellschaft
- University of Melbourne
- 270089
- European Research Council (ERC)
- European Research Area Network for Coordinating Action in Plant Sciences (ERA-CAPS)
- Created
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2016-01-20Created from EPrint's datestamp field
- Updated
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2022-05-13Created from EPrint's last_modified field