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Computational Biology and Chemistry
Volume 29, Issue 4, August 2005, Pages 288-293
 
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doi:10.1016/j.compbiolchem.2005.06.004    How to Cite or Link Using DOI (Opens New Window)
Copyright © 2005 Elsevier Ltd All rights reserved.

Exploiting scale-free information from expression data for cancer classification

Alexey V. Antonova, Corresponding Author Contact Information, E-mail The Corresponding Author, Igor V. Tetkoa, b, Denis Kosykha, Dmitrij Surmelia and Hans-Werner Mewesa, c

aGSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany bInstitute of Bioorganic and Petroleum Chemistry, Murmanskaya 1, Kyiv 02094, Ukraine cDepartment of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85350 Freising, Germany

Received 22 April 2005; 
revised 20 June 2005; 
accepted 21 June 2005. 
Available online 21 July 2005.

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Abstract

Most studies concerning expression data analyses usually exploit information on the variability of gene intensity across samples. This information is sensitive to initial data processing, which affects the final conclusions. However expression data contains scale-free information, which is directly comparable between different samples. We propose to use the pairwise ratio of gene expression values rather than their absolute intensities for a classification of expression data. This information is stable to data processing and thus more attractive for classification analyses. In proposed schema of data analyses only information on relative gene expression levels in each sample is exploited. Testing on publicly available datasets leads to superior classification results.

Keywords: Cancer classification; Expression data; Microarray data; Scale-free schema; Genes pairwise ratio

Article Outline

1. Introduction
2. Methods
3. Results
3.1. Microarray data
3.1.1. Multiple tumor type data (MTT)
3.1.2. Malignant gliomas (MG)
3.1.3. Breast cancer (BC)
3.2. Classification results
4. Discussion
Acknowledgements
References



 
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