Gene expression analysis reveals a gene set discriminatory to different metals in soil.
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.
Department of Animal Ecology, Institute of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands. benjamin.nota@gmail.com
Benjamin
B
Nota
Rudo A
RA
Verweij
Douwe
D
Molenaar
Bauke
B
Ylstra
Nico M
NM
van Straalen
Dick
D
Roelofs
D000818:Animals; D001181:Arthropods / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D019476:Insect Proteins / Q000235:genetics / Q000378:metabolism; D007928:Lethal Dose 50; D019216:Metals, Heavy / Q000633:toxicity*; D046228:Microarray Analysis; D015203:Reproducibility of Results; D012989:Soil Pollutants / Q000633:toxicity*; D018675:Toxicity Tests; D043922:Toxicogenetics / Q000379:methods; D014158:Transcription, Genetic
D019476:Insect Proteins; D019216:Metals, Heavy; D012989:Soil Pollutants