Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data

Environmental Science and Technology

Volumn 46, Issue 1, 2012, Pages 19-26

  Gong, Ping ^a   Loh, Po Ru ^b   Barker, Natalie D ^a   Tucker, George ^b   Wang, Nan ^c   Zhang, Chenhua ^d   Escalon, B Lynn ^e   Berger, Bonnie ^b   Perkins, Edward J ^e  

^a SpecPro Inc   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF SOUTHERN MISSISSIPPI   (United States)

^d University of Southern Mississippi   (United States)

^e U S ARMY ENGINEER RESEARCH AND DEVELOPMENT CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1 ,3 ,5-TRINITRO-1 ,3 ,5-TRIAZACYCLOHEXANE; 2 ,4 ,6-TRINITROTOLUENE; CHEMICAL RESIDUES; COMPUTATIONAL APPROACH; DATA SETS; DYNAMIC PROCESS; EARTHWORM EISENIA FETIDA; ENVIRONMENTAL CONCERNS; EXPRESSION PROFILE; HIGH-DIMENSIONAL; LEAST ABSOLUTE SHRINKAGE AND SELECTION OPERATORS; MICROARRAY GENE EXPRESSION DATA; MODEL EVALUATION; ORDERED PARTITIONING; PREDICTION ACCURACY; PREDICTIVE MODELING; PREDICTIVE MODELS; QUANTITATIVE PREDICTION; RANDOM FORESTS; SOIL CONTAMINATION; TESTING GROUNDS; TISSUE RESIDUE; VARIABLE SELECTION; WILCOXON RANK-SUM TESTS;

ANIMALS; CHEMICAL COMPOUNDS; COMPUTATIONAL METHODS; DECISION TREES; FORECASTING; GEOLOGIC MODELS; MATHEMATICAL MODELS; SOIL TESTING; STATISTICAL TESTS; TISSUE;

GENE EXPRESSION;

CYCLONITE; TRINITROTOLUENE;

ARRAY; BIOLOGICAL UPTAKE; COMPUTER SIMULATION; DATA SET; EARTHWORM; GENE EXPRESSION; MEASUREMENT METHOD; NUMERICAL MODEL; ORGANIC COMPOUND; POLLUTION EXPOSURE; PREDICTION; QUANTITATIVE ANALYSIS; SOIL POLLUTION; TRANSFORMATION;

ACCURACY; ARTICLE; EARTHWORM; EISENIA FETIDA; GENE EXPRESSION; MICROARRAY ANALYSIS; NONHUMAN; SOIL POLLUTION; TISSUES; TRANSCRIPTOMICS;

ANIMALS; DATABASES, GENETIC; DNA PROBES; ENVIRONMENTAL MONITORING; EXPLOSIVE AGENTS; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; OLIGOCHAETA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; REPRODUCIBILITY OF RESULTS; SURVIVAL ANALYSIS; TOXICITY TESTS; TRIAZINES; TRINITROTOLUENE;

ANIMALIA; EISENIA FETIDA;

EID: 84855324436     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es201187u     Document Type: Article

References (19)

1. Lipnick, R. L. Structure-activity relationships. In Fundamentals of Aquatic Toxicology. II. Effects, Environmental Fate, and Risk Assessment; Rand, G. M., Ed.; Taylor & Francis: Bristol, PA, 1995; pp 609-665.
2. McCarty, L. S.; Landrum, P. F.; Luoma, S. N.; Meador, J. P.; Merten, A. A.; Shephard, B. K.; van Wezel, A. P. Advancing environmental toxicology through chemical dosimetry: External exposures versus tissue residues Integr. Environ. Assess. Manage. 2011, 7 (1) 7-27
3. Meador, J. P.; Adams, W. J.; Escher, B. I.; McCarty, L. S.; McElroy, A. E.; Sappington, K. G. The tissue residue approach for toxicity assessment: findings and critical reviews from a Society of Environmental Toxicology and Chemistry Pellston Workshop Integr. Environ. Assess. Manage. 2011, 7 (1) 2-6
4. Escher, B. I.; Ashauer, R.; Dyer, S.; Hermens, J. L.; Lee, J. H.; Leslie, H. A.; Mayer, P.; Meador, J. P.; Warne, M. S. Crucial role of mechanisms and modes of toxic action for understanding tissue residue toxicity and internal effect concentrations of organic chemicals Integr. Environ. Assess. Manage. 2011, 7 (1) 28-49
5. U.S. Environmental Protection Agency. Potential Implications of Genomics for Regulatory and Risk Assessment Applications at EPA; U.S. Environmental Protection Agency: Washington, DC, 2004.
6. Van Aggelen, A. G.; Ankley, G. T.; Baldwin, W. S.; Bearden, D. W.; Benson, W. H.; Chipman, J. K.; Collette, T. W.; Craft, J. A.; Denslow, N. D.; Embry, M. R.; Falciani, F.; George, S. G.; Helbing, C. C.; Hoekstra, P. F.; Iguchi, T.; Kagami, Y.; Katsiadaki, I.; Kille, P.; Liu, L.; Lord, P. G.; McIntyre, T.; O'Neill, A.; Osachoff, H.; Perkins, E. J.; Santos, E. M.; Skirrow, R. C.; Snape, J. R.; Tyler, C. R.; Versteeg, D.; Viant, M. R.; Volz, D. C.; Williams, T. D.; Yu, L. Integrating omic technologies into aquatic ecological risk assessment and environmental monitoring: Hurdles, achievements, and future outlook Environ. Health Perspect. 2010, 118 (1) 1-5
7. Li, Y.; Wang, N.; Perkins, E. J.; Zhang, C.; Gong, P. Identification and optimization of classifier genes from multi-class earthworm microarray dataset PLoS One 2010, 5 (10) e13715
8. Tibshirani, R. Regression shrinkage and selection via the Lasso J. Royal Stat. Soc. Ser. B (Methodological) 1996, 58 (1) 267-288
9. Breiman, L. Random Forests Machine Learning 2001, 45 (1) 5-32
10. van der laan, M. J.; Pollard, K. S. A new algorithm for hybrid clustering of gene expression data with visualization and the bootstrap J. Stat. Plan. Inference 2003, 117 (2) 275-303
11. Gong, P.; Escalon, B. L.; Hayes, C. A.; Perkins, E. J. Uptake of hexanitrohexaazaisowurtzitane (CL-20) by the earthworm Eisenia fetida through dermal contact Sci. Total Environ. 2008, 390 (1) 295-299
12. Dodard, S. G.; Powlowski, J.; Sunahara, G. I. Biotransformation of 2,4,6-trinitrotoluene (TNT) by enchytraeids (Enchytraeus albidus) in vivo and in vitro Environ. Pollut. 2004, 131 (2) 263-273
13. Stenuit, B. A.; Agathos, S. N. Microbial 2,4,6-trinitrotoluene degradation: Could we learn from (bio)chemistry for bioremediation and vice versa? Appl. Microbiol. Biotechnol. 2010, 88 (5) 1043-1064
14. Pirooznia, M.; Gong, P.; Guan, X.; Inouye, L. S.; Yang, K.; Perkins, E. J.; Deng, Y. Cloning, analysis and functional annotation of expressed sequence tags from the earthworm Eisenia fetida BMC Bioinform. 2007, 8 (Suppl 7) S7
15. Gong, P.; Pirooznia, M.; Guan, X.; Perkins, E. J. Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida PLoS One 2010, 5 (12) e14266
16. Friedman, J.; Hastie, T.; Tibshirani, R. Regularization paths for generalized linear models via coordinate descent J. Stat. Softw. 2010, 33 (1) 1-22
17. Liaw, A.; Wiener, M. Classification and regression by randomForest R News 2002, 2 (3) 18-22
18. Robertson, B. K.; Jjemba, P. K. Enhanced bioavailability of sorbed 2,4,6-trinitrotoluene (TNT) by a bacterial consortium Chemosphere 2005, 58 (3) 263-270
19. Sano, H.; Wada, S.; Eguchi, H.; Osaki, A.; Saeki, T.; Nishiyama, M. Quantitative prediction of tumor response to neoadjuvant chemotherapy in breast cancer: Novel marker genes and prediction model using the expression levels Breast Cancer 2011, (DOI: 10.1007/s12282-011-0263-8)