ArticlePlant physiology2011
Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice.
Article in Plant physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
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70 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
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- A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation.Plants (Basel, Switzerland) · 2023Review
- Identification of growth regulators using cross-species network analysis in plants.Plant physiology · 2022Article
- Unraveling the Biosynthesis of Carvacrol in Different Tissues ofInternational journal of molecular sciences · 2022Article
- Lipidomics-Assisted GWAS (lGWAS) Approach for Improving High-Temperature Stress Tolerance of Crops.International journal of molecular sciences · 2022Review
- Addressing noise in co-expression network construction.Briefings in bioinformatics · 2022Review
- qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE).BMC bioinformatics · 2021Article
- Conserved co-functional network between maize and Arabidopsis aid in the identification of seed defective genes in maize.Genes & genomics · 2021Article
- Juxtapose: a gene-embedding approach for comparing co-expression networks.BMC bioinformatics · 2021Article
- Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.Frontiers in genetics · 2021Review
- The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns.Frontiers in plant science · 2021Article
- Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs.BMC genomics · 2020Article
- Interactive Gene Expression Patterns of Susceptible and ResistantFrontiers in microbiology · 2020Article
- Overexpression of rice F-box protein OsFBX322 confers increased sensitivity to gamma irradiation in Arabidopsis.Genetics and molecular biology · 2020Article
- Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics.BMC genomics · 2019Article
10 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.
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