Journal Article

Gene Expression Analysis Reveals a Gene Set Discriminatory to Different Metals in Soil

Benjamin Nota, Rudo A. Verweij, Douwe Molenaar, Bauke Ylstra, Nico M. van Straalen and Dick Roelofs

in Toxicological Sciences

Volume 115, issue 1, pages 34-40
Published in print May 2010 | ISSN: 1096-6080
Published online February 2010 | e-ISSN: 1096-0929 | DOI:
Gene Expression Analysis Reveals a Gene Set Discriminatory to Different Metals in Soil

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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.

Keywords: classifier analysis; metal; microarray; soil; springtail; toxicogenomics

Journal Article.  5119 words.  Illustrated.

Subjects: Medical Toxicology ; Toxicology (Non-medical)

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