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Integrating phenotypic and expression profiles to map arsenic-response networks

Astrid C Haugen1, Ryan Kelley2, Jennifer B Collins3, Charles J Tucker3, Changchun Deng4, Cynthia A Afshari3, J Martin Brown4, Trey Ideker2* and Bennett Van Houten1*

Author Affiliations

1 Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA

2 Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA

3 National Center for Toxicogenomics, Microarray Center, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA

4 Department of Radiation Oncology, Stanford University School of Medicine, 269 Campus Drive West, Stanford, CA 94305, USA

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Genome Biology 2004, 5:R95  doi:10.1186/gb-2004-5-12-r95

Published: 29 November 2004

Additional files

Additional data file 1:

The dose-response curve of S. cerevisiae strain, BY4741

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Additional data file 2:

A self-organized tree of arsenite treated yeast experiments and a table depicting the numbers of significant genes

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Additional data file 3:

The primary raw cDNA data from all the experiments

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Additional data file 4:

The primary raw data for all the deletion experiments

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Additional data file 5:

The ranked arsenite sensitivity (phenotypic profiling) data

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Additional data file 6:

Genes two-fold or more differentially expressed after arsenite in the Yap1 deletion strain compared to the parent

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Additional data file 7:

Genes two-fold or more differentially expressed after arsenite in the Cad1 deletion strain compared to the parent

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Additional data file 8:

Genes failing to be induced or repressed by arsenite in the Yap1 deleted strain

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Additional data file 9:

Genes failing to be induced or repressed by arsenite in the Cad1 deleted strain

Format: XLS Size: 30KB Download file

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Additional data file 10:

Under arsenite-treated conditions, Yap1 might regulate Arr2 and Arr3, and does not regulate Rpn4

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Additional data file 11:

Genes two-fold or more differentially expressed after arsenite in the Rpn4 deletion strain compared to the parent

Format: XLS Size: 150KB Download file

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Additional data file 12:

Genes failing to be induced or repressed by arsenite in the Rpn4 deleted strain

Format: XLS Size: 153KB Download file

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Additional data file 13:

Genes two-fold or more differentially expressed after arsenite in the Arr1 deletion strain compared to the parent

Format: XLS Size: 291KB Download file

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Additional data file 14:

Genes failing to be induced or repressed by arsenite in the Arr1 deleted strain

Format: XLS Size: 332KB Download file

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Additional data file 15:

Self-organized clustering of deletion strains with AsIII treatment and parent strain vs. deletion strains without arsenic

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Additional data file 16:

Gene list of two-fold differential expression in yap1Δ vs. parent without arsenic treatment

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Additional data file 17:

Gene list of two-fold differential expression in cad1Δ vs. parent without arsenic treatment

Format: XLS Size: 17KB Download file

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Additional data file 18:

Gene list of two-fold differential expression in rpn4Δ vs. parent without arsenic treatment

Format: XLS Size: 79KB Download file

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Additional data file 19:

Gene list of two-fold differential expression in arr1Δ vs. parent without arsenic treatment

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Additional data file 20:

A file of all the genes mentioned in the paper

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