ArticleBMC research notes2013
Genomic positions of co-expressed genes: echoes of chromosome organisation in gene expression data.
Article in BMC research notes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed.
- Protein family neighborhood analyzer-ProFaNA.PeerJ · 2023Article
- The Performance Comparison of Gene Co-expression Networks of Breast and Prostate Cancer using Different Selection Criteria.Interdisciplinary sciences, computational life sciences · 2021Article
- Comparative analysis of metabolic and transcriptomic features ofJournal of the Royal Society, Interface · 2020Article
- The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses.Viruses · 2019Article
- Gene expression dysregulation domains are not a specific feature of Down syndrome.Nature communications · 2019Article
- Genomic Clustering of differential DNA methylated regions (epimutations) associated with the epigenetic transgenerational inheritance of disease and phenotypic variation.BMC genomics · 2016Article
- Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe relationships between gene expression and nuclear structure, chromosome territories in particular, are currently being elucidated experimentally. Each chromosome occupies an individual, spatially-limited space with a preferential position relative to the nuclear centre that may be specific to the cell and tissue type. We sought to discover whether patterns in gene expression databases might exist that would mirror prevailing or recurring nuclear structure patterns, chromosome territory interactions in particular.
resultsWe used human gene expression datasets, both from a tissue expression atlas and from a large set including diverse types of perturbations. We identified groups of positional gene clusters over-represented in gene expression clusters. We show that some pairs of chromosomes and pairs of 10 Mbp long chromosome regions are significantly enriched in the expression clusters. The functions of genes involved in inter-chromosome co-expression relationships are non-random and predominantly related to cell-cell communication and reaction to external stimuli.
conclusionsWe suggest that inter-chromosomal gene co-expression can be interpreted in the context of nuclear structure, and that even expression datasets that include very diverse conditions and cell types show consistent relationships.
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Registered trials
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