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Open Access Research

Cancer classification: Mutual information, target network and strategies of therapy

Wen-Chin Hsu12, Chan-Cheng Liu4, Fu Chang4 and Su-Shing Chen13*

Author Affiliations

1 System Biology Lab, University of Florida, Florida, USA

2 Department of Electrical and Computer Engineering, University of Florida, Florida, USA

3 Department of Computer and Information Science and Engineering, University of Florida, Florida, USA

4 Institute of Information Science, Academia Sinica, Taipei, Taiwan

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Journal of Clinical Bioinformatics 2012, 2:16  doi:10.1186/2043-9113-2-16

Published: 2 October 2012

Abstract

Background

Cancer therapy is a challenging research area because side effects often occur in chemo and radiation therapy. We intend to study a multi-targets and multi-components design that will provide synergistic results to improve efficiency of cancer therapy.

Methods

We have developed a general methodology, AMFES (Adaptive Multiple FEature Selection), for ranking and selecting important cancer biomarkers based on SVM (Support Vector Machine) classification. In particular, we exemplify this method by three datasets: a prostate cancer (three stages), a breast cancer (four subtypes), and another prostate cancer (normal vs. cancerous). Moreover, we have computed the target networks of these biomarkers as the signatures of the cancers with additional information (mutual information between biomarkers of the network). Then, we proposed a robust framework for synergistic therapy design approach which includes varies existing mechanisms.

Results

These methodologies were applied to three GEO datasets: GSE18655 (three prostate stages), GSE19536 (4 subtypes breast cancers) and GSE21036 (prostate cancer cells and normal cells) shown in. We selected 96 biomarkers for first prostate cancer dataset (three prostate stages), 72 for breast cancer (luminal A vs. luminal B), 68 for breast cancer (basal-like vs. normal-like), and 22 for another prostate cancer (cancerous vs. normal. In addition, we obtained statistically significant results of mutual information, which demonstrate that the dependencies among these biomarkers can be positive or negative.

Conclusions

We proposed an efficient feature ranking and selection scheme, AMFES, to select an important subset from a large number of features for any cancer dataset. Thus, we obtained the signatures of these cancers by building their target networks. Finally, we proposed a robust framework of synergistic therapy for cancer patients. Our framework is not only supported by real GEO datasets but also aim to a multi-targets/multi-components drug design tool, which improves the traditional single target/single component analysis methods. This framework builds a computational foundation which can provide a clear classification of cancers and lead to an efficient cancer therapy.

Keywords:
Feature selection; Biomarkers; Microarray; Therapy design; Target network