ArticlePlant molecular biology2007
Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains.
Article in Plant molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution.Nature plants · 2022Article
- Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure.Nature plants · 2020Article
- Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.Genome biology · 2015Article
- Current challenges and future potential of tomato breeding using omics approaches.Breeding science · 2013Article
- Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice.Functional & integrative genomics · 2012Article
- A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat.Plant physiology · 2011Article
- Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice.Plant physiology · 2011Article
- Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation.Genome biology · 2011Article
- Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes.BMC genomics · 2010Article
- Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions.BMC genomics · 2010Article
- Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response.BMC genomics · 2009Article
- Structure and expression analysis of rice paleo duplications.Nucleic acids research · 2009Article
- Comparative genomics of grasses promises a bountiful harvest.Plant physiology · 2009Article
- Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and populus.Plant physiology · 2008Article
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3 authors.
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Abstract
Chromosomal coexpression domains are found in a number of different genomes under various developmental conditions. The size of these domains and the number of genes they contain vary. Here, we define local coexpression domains as adjacent genes where all possible pair-wise correlations of expression data are higher than 0.7. In rice, such local coexpression domains range from predominantly two genes, up to 4, and make up approximately 5% of the genomic neighboring genes, when examining different expression platforms from the public domain. The genes in local coexpression domains do not fall in the same ontology category significantly more than neighboring genes that are not coexpressed. Duplication, orientation or the distance between the genes does not solely explain coexpression. The regulation of coexpression is therefore thought to be regulated at the level of chromatin structure. The characteristics of the local coexpression domains in rice are strikingly similar to such domains in the Arabidopsis genome. Yet, no microsynteny between local coexpression domains in Arabidopsis and rice could be identified. Although the rice genome is not yet as extensively annotated as the Arabidopsis genome, the lack of conservation of local coexpression domains may indicate that such domains have not played a major role in the evolution of genome structure or in genome conservation.
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