ArticlePlant physiology2005
Local coexpression domains of two to four genes in the genome of Arabidopsis.
Article in Plant physiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 55 citations in OpenAlex.
- Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.Genome biology · 2015Article
- Coexpression patterns indicate that GPI-anchored non-specific lipid transfer proteins are involved in accumulation of cuticular wax, suberin and sporopollenin.Plant molecular biology · 2013Article
- 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
- The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.PloS one · 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
- Gepoclu: a software tool for identifying and analyzing gene positional clusters in large-scale gene expression analysis.BMC bioinformatics · 2011Article
- Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation.Genome biology · 2011Article
- Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae.BMC genomics · 2010Article
- 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
- Co-expression of neighboring genes in the zebrafish (Danio rerio) genome.International journal of molecular sciences · 2009Article
- Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response.BMC genomics · 2009Article
- Review
- Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.PloS one · 2008Article
- Regulon organization of Arabidopsis.BMC plant biology · 2008Article
- Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and populus.Plant physiology · 2008Article
- Structures of the three homoeologous loci of wheat benzoxazinone biosynthetic genes TaBx3 and TaBx4 and characterization of their promoter sequences.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2008Article
- Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.Genome biology · 2008Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Expression of genes in eukaryotic genomes is known to cluster, but cluster size is generally loosely defined and highly variable. We have here taken a very strict definition of cluster as sets of physically adjacent genes that are highly coexpressed and form so-called local coexpression domains. The Arabidopsis (Arabidopsis thaliana) genome was analyzed for the presence of such local coexpression domains to elucidate its functional characteristics. We used expression data sets that cover different experimental conditions, organs, tissues, and cells from the Massively Parallel Signature Sequencing repository and microarray data (Affymetrix) from a detailed root analysis. With these expression data, we identified 689 and 1,481 local coexpression domains, respectively, consisting of two to four genes with a pairwise Pearson's correlation coefficient larger than 0.7. This number is approximately 1- to 5-fold higher than the numbers expected by chance. A small (5%-10%) yet significant fraction of genes in the Arabidopsis genome is therefore organized into local coexpression domains. These local coexpression domains were distributed over the genome. Genes in such local domains were for the major part not categorized in the same functional category (GOslim). Neither tandemly duplicated genes nor shared promoter sequence nor gene distance explained the occurrence of coexpression of genes in such chromosomal domains. This indicates that other parameters in genes or gene positions are important to establish coexpression in local domains of Arabidopsis chromosomes.
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