Open Access Highly Accessed Research article

Conservation of core gene expression in vertebrate tissues

Esther T Chan15, Gerald T Quon25, Gordon Chua356, Tomas Babak57, Miles Trochesset23, Ralph A Zirngibl1, Jane Aubin1, Michael JH Ratcliffe4, Andrew Wilde1, Michael Brudno235, Quaid D Morris1235* and Timothy R Hughes135*

Author Affiliations

1 Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

2 Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

3 Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

4 Department of Immunology and Sunnybrook Research Institute, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

5 Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

6 Current address: Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4 Canada

7 Current address: Rosetta Inpharmatics, 401 Terry Avenue North, Seattle, WA 98109, USA

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Journal of Biology 2009, 8:33  doi:10.1186/jbiol130

Published: 16 April 2009

Additional files

Additional data file 1:

The tissues at the top, highlighted in color, are those considered to be among the ten common tissue types. Those with identical coloring were combined (by averaging normalized intensities) for the analysis of conservation of gene expression among the ten common tissues.

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Additional data file 2:

Clustergrams show the microarray datasets in chicken, frog and pufferfish, displayed as relative expression ratio (see Materials and methods) of each gene within each of the 20 tissues profiled. Rows and columns were ordered independently for each dataset, and high-level branches broken and rearranged to obtain a diagonal appearance as described in [44].

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Additional data file 3:

Dendrogram of correlations among ten common tissues, using 1 – Pearson correlation and average linkage over 3,074 genes.

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Additional data file 4:

Selected GO biological process categories enriched amongst genes highly expressed within each of the ten common tissues in each species are shown. The tissue and GO category order were manually arranged in the heat map. (A full matrix of WMW scores is given in Additional data file 13.)

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Additional data file 5:

Binary matrix of genes classified as having fully conserved expression events, based on ranked microarray spot intensity, at five different thresholds (1/6, 1/5, 1/4, 1/3, 1/2).

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Additional data file 6:

The cumulative distributions show the proportion of all 3,074 genes with Pearson r (normalized intensities) below the value shown on the horizontal axis, for real orthologs (green) and randomly matched genes (blue).

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Additional data file 7:

Feature matrix used to compare conservation of expression measures to other attributes of individual genes, with Spearman correlations and p-values.

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Additional data file 8:

WMW p-values for categorical gene attributes, with ranks determined by relative conservation of gene expression by median Pearson correlation for each species against Tetraodon.

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Additional data file 9:

Cumulative distribution of EEL scores for real and permuted orthology between human and pufferfish.

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Additional data file 10:

Breakdown of the proportion of all genes in each species that are expressed within each tissue.

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Additional data file 11:

List of genes classified as TFs on the basis of containing a known DNA binding domain.

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Additional data file 12:

Clustergrams showing Spearman correlations and p-values for comparisons of gene expression conservation versus other gene properties.

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Additional data file 13:

SWMW enrichment p-values of genes associated with GO biological process annotations expressed within each tissue of each species (full matrix used to create Additional data file 4).

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