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A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression

Nature Genetics volume 26, pages 183–186 (2000)Cite this article

Abstract

Chromosome correlation maps display correlations between the expression patterns of genes on the same chromosome. Using these maps, we show here that adjacent pairs of genes, as well as nearby non-adjacent pairs of genes, show correlated expression independent of their orientation. We present specific examples of adjacent pairs with highly correlated expression patterns, in which the promoter of only one of the two genes contains an upstream activating sequence (UAS) known to be associated with that expression pattern. Finally, we show that genes with similar functions tend to occur in adjacent positions along the chromosomes. Our results suggest that, in certain chromosomal expression domains, an UAS can affect the transcription of genes that are not immediately downstream from it.

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Figure 1: Correlation maps for yeast chromosomes.
Figure 2: Histograms of the distributions of correlation coefficients describing the expression of divergent
Figure 3: Comparison of adjacent pairs with different orientations.
Figure 4: Relationship of the distance between the predicted start sites of adjacent ORFs and their correlation.

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Acknowledgements

We thank J. Aach, W. Rindone, S. Tavazoie, J. Graber, K. Struhl and F. Winston for advice, suggestions and data files; and P. Sudarsanam, A. Dudley, T. Pilpel, A. Derti, P. Estep, M. Steffen, V. Badarinarayana, T. Wu and M. Bulyk for discussions and critical readings of the manuscript. B.A.C. was supported by a postdoctoral fellowship from the American Cancer Society (PF-98-159-01-MBC). This work was supported by the US Department of Energy (DE-FG02-87-ER60565), the Office of Naval Research and DARPA (N00014-97-1-0865), the Lipper Foundation and Hoechst Marion Roussel.

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  1. Barak A. Cohen and Robi D. Mitra: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA

    Barak A. Cohen, Robi D. Mitra, Jason D. Hughes & George M. Church

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  1. Barak A. Cohen
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Correspondence to George M. Church.

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Cohen, B., Mitra, R., Hughes, J. et al. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26, 183–186 (2000). https://doi.org/10.1038/79896

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