Gene-specific patterns of expression variation across organs and species

Breschi, A., Djebali, S., Gillis, J., Pervouchine, D. D., Dobin, A., Davis, C. A., Gingeras, T. R., Guigo, R. (2016) Gene-specific patterns of expression variation across organs and species. Genome Biol, 17 (1). p. 151. ISSN 1474-760X (Electronic)1474-7596 (Linking)

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DOI: 10.1186/s13059-016-1008-y


BACKGROUND: A comparison of transcriptional profiles derived from different tissues in a given species or among different species assumes that commonalities reflect evolutionarily conserved programs and that differences reflect species or tissue responses to environmental conditions or developmental program staging. Apparently conflicting results have been published regarding whether organ-specific transcriptional patterns dominate over species-specific patterns, or vice versa, making it unclear to what extent the biology of a given organism can be extrapolated to another. These studies have in common that they treat the transcriptomes monolithically, implicitly ignoring that each gene is likely to have a specific pattern of transcriptional variation across organs and species. RESULTS: We use linear models to quantify this pattern. We find a continuum in the spectrum of expression variation: the expression of some genes varies considerably across species and little across organs, and simply reflects evolutionary distance. At the other extreme are genes whose expression varies considerably across organs and little across species; these genes are much more likely to be associated with diseases than are genes whose expression varies predominantly across species. CONCLUSIONS: Whether transcriptomes, when considered globally, cluster preferentially according to one component or the other may not be a property of the transcriptomes, but rather a consequence of the dominant behavior of a subset of genes. Therefore, the values of the components of the variance of expression for each gene could become a useful resource when planning, interpreting, and extrapolating experimental data from mouse to humans.

Item Type: Paper
Uncontrolled Keywords: Clustering Comparative transcriptomics Gene expression Organ RNA-seq Species Vertebrate
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:
Communities: CSHL labs > Gillis Lab
CSHL labs > Gingeras lab
CSHL labs > Dobin Lab
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
Depositing User: Matt Covey
Date: 2016
Date Deposited: 04 Aug 2016 20:04
Last Modified: 29 Oct 2020 15:30
PMCID: PMC4937605
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