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Identification and Optimization of Classifier Genes from Multi-Class Earthworm Microarray Dataset

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  • Ying Li
  • Nan Wang
  • Edward J Perkins
  • Chaoyang Zhang
  • Ping Gong

Abstract

Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes and have used it to profile gene expression in 248 earthworms exposed to TNT, RDX or neither. We assembled a new machine learning pipeline consisting of several well-established feature filtering/selection and classification techniques to analyze the 248-array dataset in order to construct classifier models that can separate earthworm samples into three groups: control, TNT-treated, and RDX-treated. First, a total of 869 genes differentially expressed in response to TNT or RDX exposure were identified using a univariate statistical algorithm of class comparison. Then, decision tree-based algorithms were applied to select a subset of 354 classifier genes, which were ranked by their overall weight of significance. A multiclass support vector machine (MC-SVM) method and an unsupervised K-mean clustering method were applied to independently refine the classifier, producing a smaller subset of 39 and 30 classifier genes, separately, with 11 common genes being potential biomarkers. The combined 58 genes were considered the refined subset and used to build MC-SVM and clustering models with classification accuracy of 83.5% and 56.9%, respectively. This study demonstrates that the machine learning approach can be used to identify and optimize a small subset of classifier/biomarker genes from high dimensional datasets and generate classification models of acceptable precision for multiple classes.

Suggested Citation

  • Ying Li & Nan Wang & Edward J Perkins & Chaoyang Zhang & Ping Gong, 2010. "Identification and Optimization of Classifier Genes from Multi-Class Earthworm Microarray Dataset," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-9, October.
  • Handle: RePEc:plo:pone00:0013715
    DOI: 10.1371/journal.pone.0013715
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    References listed on IDEAS

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    1. Michele Trabucchi & Paola Briata & MariaFlor Garcia-Mayoral & Astrid D. Haase & Witold Filipowicz & Andres Ramos & Roberto Gherzi & Michael G. Rosenfeld, 2009. "The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs," Nature, Nature, vol. 459(7249), pages 1010-1014, June.
    2. Jen-Tsan Chi & Edwin H Rodriguez & Zhen Wang & Dimitry S A Nuyten & Sayan Mukherjee & Matt van de Rijn & Marc J van de Vijver & Trevor Hastie & Patrick O Brown, 2007. "Gene Expression Programs of Human Smooth Muscle Cells: Tissue-Specific Differentiation and Prognostic Significance in Breast Cancers," PLOS Genetics, Public Library of Science, vol. 3(9), pages 1-15, September.
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