ArticlePlant physiology2016
FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.
Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls.Nature plants · 2025Article
- Coordinated regulation of the entry and exit steps of aromatic amino acid biosynthesis supports the dual lignin pathway in grasses.Nature communications · 2023Article
- Emerging Roles of Receptor-like Protein Kinases in Plant Response to Abiotic Stresses.International journal of molecular sciences · 2023Review
- Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs.BMC plant biology · 2022Article
- Exploiting plant transcriptomic databases: Resources, tools, and approaches.Plant communications · 2022Review
- A G protein-coupled receptor-like module regulates cellulose synthase secretion from the endomembrane system in Arabidopsis.Developmental cell · 2021Article
- LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data.BMC biology · 2020Article
- Characterization of In Vivo Function(s) of Members of the Plant Mitochondrial Carrier Family.Biomolecules · 2020Review
- Metabolic Roles of Plant Mitochondrial Carriers.Biomolecules · 2020Review
- Cross-Species Comparison of Fruit-Metabolomics to Elucidate Metabolic Regulation of Fruit Polyphenolics Among Solanaceous Crops.Metabolites · 2020Article
- Article
- Expression Atlas ofThe Plant cell · 2020Article
- The evolution of metabolism: How to test evolutionary hypotheses at the genomic level.Computational and structural biotechnology journal · 2020Review
- Genomics of Evolutionary Novelty in Hybrids and Polyploids.Frontiers in genetics · 2020Review
- Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom.Computational and structural biotechnology journal · 2020Article
- Using Gene Expression to Study Specialized Metabolism-A Practical Guide.Frontiers in plant science · 2020Review
- Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.Nature communications · 2019Article
- Comparing time series transcriptome data between plants using a network module finding algorithm.Plant methods · 2019Article
- PhytoNet: comparative co-expression network analyses across phytoplankton and land plants.Nucleic acids research · 2018Article
- CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.Nucleic acids research · 2018Article
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9 authors.
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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.
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