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A classification based framework for quantitative description of large-scale microarray data

Dipen P Sangurdekar12, Friedrich Srienc12 and Arkady B Khodursky23*

Author Affiliations

1 Department of Chemical Engineering and Materials Science, University of Minnesota, Saint Paul, MN 55108, USA

2 Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA

3 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, MN 55108, USA

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Genome Biology 2006, 7:R32  doi:10.1186/gb-2006-7-4-r32

Published: 20 April 2006

Additional files

Additional File 1:

Figure S1. Ribosomal and Heat shock genes; Figure S2. Drug (DNA damaging) comparisons; Figure S3. Norfloxacin treatment in resistant strains; Figure S4: Profile of RpoS subgroup in all conditions; Figure S5. Signature classes in LB recovery conditions; Figure S6. Growth conditions comparison; Figure S7. Drug (non-DNA damaging) comparisons; Figure S8. Simulated expression profiles for comparison of methods

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Additional File 2:

Scores of top classes in antibiotic and radiation treatments

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Additional File 3:

Top class scores in growth and recovery conditions

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Additional File 4:

Comparison of results obtained from entropy reduction and SA

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Additional File 5:

Classes and corresponding genes used in the analysis

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Additional File 6:

Description of SVD and the method of entropy calculation

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Additional File 7:

Log ratio expression data

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Additional File 8:

Conditions used in this analysis and their descriptions

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Additional File 9:

Sample data files are in a compressed (zip) format

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