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

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

doi:10.1038/79896

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

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

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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.

Original language	English
Pages (from-to)	183-186
Number of pages	4
Journal	Nature Genetics
Volume	26
Issue number	2
DOIs	https://doi.org/10.1038/79896
State	Published - Oct 2000

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@article{34187818aafd439d988040e88aa17730,

title = "A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression",

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.",

author = "Cohen, {Barak A.} and Mitra, {Robi D.} and Hughes, {Jason D.} and Church, {George M.}",

note = "Funding Information: 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.",

year = "2000",

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doi = "10.1038/79896",

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pages = "183--186",

journal = "Nature Genetics",

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AU - Cohen, Barak A.

AU - Mitra, Robi D.

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N1 - Funding Information: 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.

PY - 2000/10

Y1 - 2000/10

N2 - 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.

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

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