ArticlePlant physiology2010
The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks.
Article in Plant physiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Phylogenomic Insights into High Conservation and Lineage-Specific Expansion of the ABAPT Gene Family in Plants.International journal of molecular sciences · 2026Article
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- Deciphering the role of lncRNA-mediated ceRNA network in disuse osteoporosis: insights from bone marrow mesenchymal stem cells under simulated microgravity.Frontiers in medicine · 2025Article
- Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits.G3 (Bethesda, Md.) · 2024Article
- Exploring large-scale gene coexpression networks in peach (Horticulture research · 2024Article
- A systems genomics and genetics approach to identify the genetic regulatory network for lignin content inFrontiers in plant science · 2024Article
- A gene network-driven approach to infer novel pathogenicity-associated genes: application tomSystems · 2023Article
- Soybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development.Molecular plant pathology · 2023Article
- Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Genes · 2022Article
- Gene Co-expression Network Analysis and Linking Modules to Phenotyping Response in Plants.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses.Plants (Basel, Switzerland) · 2021Article
- Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs.BMC genomics · 2020Article
- Construction, comparison and evolution of networks in life sciences and other disciplines.Journal of the Royal Society, Interface · 2020Article
- TGCnA: temporal gene coexpression network analysis using a low-rank plus sparse framework.Journal of applied statistics · 2020Article
- Network-based feature selection reveals substructures of gene modules responding to salt stress in rice.Plant direct · 2019Article
- Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius.Plant molecular biology · 2018Article
- Identification of key gene modules for human osteosarcoma by co-expression analysis.World journal of surgical oncology · 2018Article
- Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study.Scientific reports · 2017Article
- Suppressive effect of microRNA319 expression on rice plant height.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- The Relationship between Selection, Network Connectivity, and Regulatory Variation within a Population of Capsella grandiflora.Genome biology and evolution · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Discovering gene sets underlying the expression of a given phenotype is of great importance, as many phenotypes are the result of complex gene-gene interactions. Gene coexpression networks, built using a set of microarray samples as input, can help elucidate tightly coexpressed gene sets (modules) that are mixed with genes of known and unknown function. Functional enrichment analysis of modules further subdivides the coexpressed gene set into cofunctional gene clusters that may coexist in the module with other functionally related gene clusters. In this study, 45 coexpressed gene modules and 76 cofunctional gene clusters were discovered for rice (Oryza sativa) using a global, knowledge-independent paradigm and the combination of two network construction methodologies. Some clusters were enriched for previously characterized mutant phenotypes, providing evidence for specific gene sets (and their annotated molecular functions) that underlie specific phenotypes.
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