ArticleScientific reports2016
Pan- and core- network analysis of co-expression genes in a model plant.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Integrative gene co-expression network analysis reveals protein-coding and LncRNA genes associated with Alzheimer's disease pathology.Scientific reports · 2025Article
- The skimmed milk proteome of dairy cows is affected by the stage of lactation and by supplementation with polyunsaturated fatty acids.Scientific reports · 2024Article
- A method for mining condition-specific co-expressed genes in Camellia sinensis based on k-means clustering.BMC plant biology · 2024Article
- Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits.G3 (Bethesda, Md.) · 2024Article
- Co-expression pan-network reveals genes involved in complex traits within maize pan-genome.BMC plant biology · 2022Article
- In search of a Drosophila core cellular network with single-cell transcriptome data.G3 (Bethesda, Md.) · 2022Article
- Approaches in Gene Coexpression Analysis in Eukaryotes.Biology · 2022Review
- Gene Co-Expression Network Tools and Databases for Crop Improvement.Plants (Basel, Switzerland) · 2022Review
- Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits.Frontiers in plant science · 2022Article
- Article
- Comparative co-expression network analysis extracts thePlant biotechnology (Tokyo, Japan) · 2019Article
- Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana.Planta · 2019Article
- Identification of gene expression logical invariants inPlant direct · 2019Article
- A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization.Frontiers in plant science · 2019Article
- PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System.Genomics, proteomics & bioinformatics · 2018Article
- Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study.Scientific reports · 2017Article
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2 authors.
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Abstract
Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of 'pan-network' and 'core-network' representing union and intersection between a sizeable fractions of individual networks, respectively. We showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.
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