ArticleBMC genomics2004
Inter-species differences of co-expression of neighboring genes in eukaryotic genomes.
Article in BMC genomics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- Identification of an atypical microRNA with sequence variation in the silkworm Bombyx mori.PloS one · 2026Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.PLoS computational biology · 2021Article
- Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells.PLoS genetics · 2019Article
- Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate.Frontiers in genetics · 2019Article
- Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes.BMC genomics · 2018Article
- Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions.Nature communications · 2018Article
- Analysis of the relationship between coexpression domains and chromatin 3D organization.PLoS computational biology · 2017Article
- A Preliminary Study on the Pattern, the Physiological Bases and the Molecular Mechanism of the Adductor Muscle Scar Pigmentation in Pacific OysterFrontiers in physiology · 2017Article
- Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.The EMBO journal · 2015Review
- Neighboring Genes Show Correlated Evolution in Gene Expression.Molecular biology and evolution · 2015Article
- The clustering of functionally related genes contributes to CNV-mediated disease.Genome research · 2015Article
- Expression-based segmentation of the Drosophila genome.BMC genomics · 2013Article
- Chapter 15: disease gene prioritization.PLoS computational biology · 2013Article
- Genome-wide prediction and functional validation of promoter motifs regulating gene expression in spore and infection stages of Phytophthora infestans.PLoS pathogens · 2013Article
- Widespread promoter-mediated coordination of transcription and mRNA degradation.Genome biology · 2012Article
- Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.Genome research · 2012Article
- Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution.Eukaryotic cell · 2012Review
- Intrinsic features of Aedes aegypti genes affect transcriptional responsiveness of mosquito genes to dengue virus infection.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundThere is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human.
resultsWe analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8-30 % of the highly co-expressed pairs are duplicated genes.
conclusionWe confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.
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