A three-stage algorithm to make toxicologically relevant activity calls from quantitative high throughput screening data

Environmental Health Perspectives

Volumn 120, Issue 8, 2012, Pages 1107-1115

  Shockley, Keith R ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

Activity calls; Concentration response; Hill equation; Quantitative high throughput screening; Tox21

Indexed keywords

ANDROGEN RECEPTOR;

AREA UNDER THE CURVE; ARTICLE; CLASSIFICATION ALGORITHM; CONCENTRATION RESPONSE; ERROR; HIGH THROUGHPUT SCREENING; HUMAN; LINEAR REGRESSION ANALYSIS; NONBIOLOGICAL MODEL; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SAMPLE SIZE; SIMULATION; STUDENT T TEST; TOXICOLOGY;

ALGORITHMS; ANDROGENS; HAZARDOUS SUBSTANCES; HIGH-THROUGHPUT SCREENING ASSAYS;

EID: 84864750654     PISSN: 00916765     EISSN: 15529924     Source Type: Journal    
DOI: 10.1289/ehp.1104688     Document Type: Article

References (22)

1. Collins FS, Gray GM, Bucher JR. 2008. Toxicology. Transforming environmental health protection. Science 319:906-907.
2. Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA. 2005. Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 6:59-75.
3. Fawcett T. 2006. An introduction to ROC analysis. Pattern Recognit Lett 27:861-874.
4. Hill AV. 1910. The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40:4-7.
5. Huang R, Southall N, Cho M-H, Xia M, Inglese J, Austin CP. 2008. Characterization of diversity in toxicity mechanism using in vitro cytotoxicity assays in quantitative high throughput screening. Chem Res Toxicol 21:659-667.
6. Huang R, Xia M, Cho MH, Sakamuru S, Shinn P, Houck KA, et al. 2011. Chemical genomics profiling of environmental chemical modulation of human nuclear receptors. Environ Health Perspect 119:1142-1148.
7. Inglese J, Auld DS, Jadhav A, Johnson RL, Simeonov A, Yasgar A, et al. 2006. Quantitative high-throughput screening: a titration-based approach that efficiently identifies biological activities in large chemical libraries. Proc Natl Acad Sci USA 103:11473-11478.
8. Johnson RL, Huang R, Jadhav A, Southall N, Wichterman J, MacArthur R, et al. 2009. A quantitative high-throughput screen for modulators of IL-6 signaling: a model for interrogating biological networks using chemical libraries. Mol Biosyst 5:1039-1050.
9. Judson R, Richard A, Dix D, Houck K, Elloumi F, Martin M, et al. 2008. ACToR-Aggregated computational toxicology resource. Toxicol Appl Pharmacol 233:7-13.
10. Judson RS, Houck KA, Kavlock RJ, Knudsen TB, Martin MT, Mortensen HM, et al. 2010. In vitro screening of environmental chemicals for targeted testing prioritization-the ToxCast project. Environ Health Perspect 118:485-492.
11. Martin MT, Knudsen TB, Reif DM, Houck KA, Judson RS, Kavlock RJ, et al. 2011. Predictive model of rat reproductive toxicity from ToxCast high throughput screening. Biol Reprod 85:327-339.
12. Muir DC, Howard PH. 2006. Are there other persistent organic pollutants? A challenge for environmental chemists. Environ Sci Technol 40:7157-7166.
13. Parham F, Austin C, Southall N, Huang R, Tice R, Portier C. 2009. Dose-response modeling of high-throughput screening data. J Biomol Screen 14:1216-1227.
14. Reif D, Martin M, Tan S, Houck K, Judson R, Richard A, et al. 2010. Endocrine profiling and prioritization of environmental chemical using ToxCast data. Environ Health Perspect 118:1714-1720.
15. Ritz C, Streibig JC. 2005. Bioassay analysis using R. J Stat Softw 12:1-22.
16. Shukla SJ, Huang R, Austin CP, Xia M. 2010. Foundation review: The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform. Drug Discov Today 15:997-1007.
17. Smyth GK. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3(1):1544-6115.
18. Tuszynski J. 2009. CaTools: Tools: moving window statistics, GOF, Base64, ROC AUC, etc. R package version 1.10. Available: http://CRAN.R-project.org/package=caTools [accessed 28 May 2010].
19. Venables WN, Ripley BD. 2002. Modern applied statistics with S, 4th ed. New York:Springer.
20. Wang Y, Jadhav A, Southal N, Huang R, Nguyen DT. 2010. A grid algorithm for high throughput fitting of dose-response curve data. Curr Chem Genomics 4:57-66.
21. Waters M, Stasiewicz S, Merrick BA, Tomer K, Bushel P, Paules R, et al. 2008. CEBS-Chemical effects in biological systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res 36:D892-D900.
22. Zhang X, Newsted JL, Hecker M, Higley EB, Jones PD, Giesy JP. 2009. Classification of chemicals based on concentration-dependent toxicological data using ToxClust. Environ Sci Technol 43:3926-3932.