Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants

Research output: Contribution to journalArticle

Standard

Harvard

APA

Vancouver

Author

Bibtex

@article{98bd286897d64a2a83966a9212ca049d,
title = "Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants",
abstract = "Genomic technologies offer opportunities to gain a more global assessment of the health status of an organism through an understanding of the functional pathways that are responding to pollutant exposure. We have developed a 13,000 clone cDNA toxicogenomics microarray for Platichthys flesus, the European flounder (EU-GENIPOL Project). We aimed to distinguish the origins of flounder taken from six sampling sites of different pollution status in Northern Europe according to their hepatic gene expression profile using bioinformatic approaches. To determine which gene expression differences may relate to pollutant impact, we have completed complementary laboratory exposures of flounder to selected toxicants and determined the associated gene expression profiles. Using multivariate variable selection coupled with a statistical modelling procedure (GALGO) we can predict geographical site but the accuracy is limited to specific sites. The search space for a combination of genes that effectively predicts class membership is very large, however, by combining the signatures derived from acute laboratory exposure to individual chemicals to limit the search space, a very accurate model for classification of all the different environmental sites was achieved. The final model utilised the expression profiles of 16 clones and validation with a qPCR array comprising these genes correctly assigned the site of origin for fish obtained from three of the sites in an independent sampling. These data would imply that the gene expression fingerprints obtained with these arrays are primarily attributable to variations in chemical pollutant responses at the different sites, indicating their potential utility in environmental impact assessment. (c) 2008 Elsevier B.V. All rights reserved.",
keywords = "Microarray, Ecotoxicogenomics, Flounder, GALGO, Environmental diagnostics, Pollution, Modeling",
author = "Francesco Falciani and AM Diab and V Sabine and Timothy Williams and Fernando Ortega and SG George and James Chipman",
year = "2008",
month = nov,
day = "11",
doi = "10.1016/j.aquatox.2008.07.020",
language = "English",
volume = "90",
pages = "92--101",
journal = "Aquatic Toxicology",
issn = "0166-445X",
publisher = "Elsevier",
number = "2",

}

RIS

TY - JOUR

T1 - Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants

AU - Falciani, Francesco

AU - Diab, AM

AU - Sabine, V

AU - Williams, Timothy

AU - Ortega, Fernando

AU - George, SG

AU - Chipman, James

PY - 2008/11/11

Y1 - 2008/11/11

N2 - Genomic technologies offer opportunities to gain a more global assessment of the health status of an organism through an understanding of the functional pathways that are responding to pollutant exposure. We have developed a 13,000 clone cDNA toxicogenomics microarray for Platichthys flesus, the European flounder (EU-GENIPOL Project). We aimed to distinguish the origins of flounder taken from six sampling sites of different pollution status in Northern Europe according to their hepatic gene expression profile using bioinformatic approaches. To determine which gene expression differences may relate to pollutant impact, we have completed complementary laboratory exposures of flounder to selected toxicants and determined the associated gene expression profiles. Using multivariate variable selection coupled with a statistical modelling procedure (GALGO) we can predict geographical site but the accuracy is limited to specific sites. The search space for a combination of genes that effectively predicts class membership is very large, however, by combining the signatures derived from acute laboratory exposure to individual chemicals to limit the search space, a very accurate model for classification of all the different environmental sites was achieved. The final model utilised the expression profiles of 16 clones and validation with a qPCR array comprising these genes correctly assigned the site of origin for fish obtained from three of the sites in an independent sampling. These data would imply that the gene expression fingerprints obtained with these arrays are primarily attributable to variations in chemical pollutant responses at the different sites, indicating their potential utility in environmental impact assessment. (c) 2008 Elsevier B.V. All rights reserved.

AB - Genomic technologies offer opportunities to gain a more global assessment of the health status of an organism through an understanding of the functional pathways that are responding to pollutant exposure. We have developed a 13,000 clone cDNA toxicogenomics microarray for Platichthys flesus, the European flounder (EU-GENIPOL Project). We aimed to distinguish the origins of flounder taken from six sampling sites of different pollution status in Northern Europe according to their hepatic gene expression profile using bioinformatic approaches. To determine which gene expression differences may relate to pollutant impact, we have completed complementary laboratory exposures of flounder to selected toxicants and determined the associated gene expression profiles. Using multivariate variable selection coupled with a statistical modelling procedure (GALGO) we can predict geographical site but the accuracy is limited to specific sites. The search space for a combination of genes that effectively predicts class membership is very large, however, by combining the signatures derived from acute laboratory exposure to individual chemicals to limit the search space, a very accurate model for classification of all the different environmental sites was achieved. The final model utilised the expression profiles of 16 clones and validation with a qPCR array comprising these genes correctly assigned the site of origin for fish obtained from three of the sites in an independent sampling. These data would imply that the gene expression fingerprints obtained with these arrays are primarily attributable to variations in chemical pollutant responses at the different sites, indicating their potential utility in environmental impact assessment. (c) 2008 Elsevier B.V. All rights reserved.

KW - Microarray

KW - Ecotoxicogenomics

KW - Flounder

KW - GALGO

KW - Environmental diagnostics

KW - Pollution

KW - Modeling

U2 - 10.1016/j.aquatox.2008.07.020

DO - 10.1016/j.aquatox.2008.07.020

M3 - Article

C2 - 18823667

VL - 90

SP - 92

EP - 101

JO - Aquatic Toxicology

JF - Aquatic Toxicology

SN - 0166-445X

IS - 2

ER -