Genomic positions of co-expressed genes: Echoes of chromosome organisation in gene expression data

Teresa Szczepińska, Krzysztof Pawłowski

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

Background: The 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. Results: We 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. Conclusions: We 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.

Original languageEnglish (US)
Article number229
JournalBMC Research Notes
Volume6
Issue number1
DOIs
StatePublished - 2013
Externally publishedYes

Keywords

  • Chromosome territory
  • Cluster analysis
  • Gene expression
  • Nuclear structure

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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