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

Genome Biology
Dipen P SangurdekarArkady B Khodursky

Abstract

Genome-wide surveys of transcription depend on gene classifications for the purpose of data interpretation. We propose a new information-theoretical-based method to: assess significance of co-expression within any gene group; quantitatively describe condition-specific gene-class activity; and systematically evaluate conditions in terms of gene-class activity. We applied this technique to describe microarray data tracking Escherichia coli transcriptional responses to more than 30 chemical and physiological perturbations. We correlated the nature and breadth of the responses with the nature of perturbation, identified gene group proxies for the perturbation classes and quantitatively compared closely related physiological conditions.

Associated Datasets

References

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Citations

Sep 3, 2010·Applied Microbiology and Biotechnology·Stephanie HuhnKay Marin
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Datasets Mentioned

BETA
GSE4357-GSE4380

Methods Mentioned

BETA
ISA

Software Mentioned

SOM
GenePix
MATLAB
EcoCyc
EntropyReduce
Sigma Genosys

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