Gene expression analysis reveals a gene set discriminatory to different metals in soil.

B. Nota, R.A. Verweij, D. Molenaar, B. Ylstra, N.M. van Straalen, D. Roelofs

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Environmental pollution is a worldwide problem, and metals are the largest group of contaminants in soil. Microarray toxicogenomic studies with ecologically relevant organisms, such as springtails, supplement traditional ecotoxicological research but are presently rather descriptive. Classifier analysis, a more analytical application of the microarray technique, is able to predict biological classes of unknown samples. We used the uncorrelated shrunken centroid method to classify gene expression profiles of the springtail Folsomia candida exposed to soil spiked with six different metals (barium, cadmium, cobalt, chromium, lead, and zinc). We identified a gene set (classifier) of 188 genes that can discriminate between six different metals present in soil, which allowed us to predict the correct classes for samples of an independent test set with an accuracy of 83% (error rate = 0.17). This study shows further that in order to apply classifier analysis to actual contaminated field soil samples, more insight and information is needed on the transcriptional responses of soil organisms to different soil types (properties) and mixtures of contaminants. © The Author 2010. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved.
Original languageEnglish
Pages (from-to)34-40
JournalToxicological Sciences
Volume115
Issue number1
DOIs
Publication statusPublished - 2010

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