Statistical issues in subpopulation analysis of high content imaging data

Journal of Computational Biology

Volumn 17, Issue 7, 2010, Pages 879-894

  Huang, Shuguang ^a  

^a WYETH RESEARCH   (United States)

Author keywords

classification; clustering; high content imaging; mixture model; multivariate; statistics; subpopulation

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; CYTOLOGY; IMAGE PROCESSING; METHODOLOGY; MULTIVARIATE ANALYSIS; STATISTICS; PROCEDURES;

CLUSTER ANALYSIS; CYTOLOGICAL TECHNIQUES; IMAGE PROCESSING, COMPUTER-ASSISTED; MULTIVARIATE ANALYSIS; STATISTICS AS TOPIC;

EID: 77954933505     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0071     Document Type: Article

References (36)

1. Abraham, V.C., Taylor, D.L., and Haskins, J.R. 2004. High content screening applied to large-scale cell biology. Review. Trends Biotechnol. 22, 15-22.
2. Baldetorp, B., Dalberg, M., Holst, U., et al. 1989. Statistical evaluation of cell kinetic data from DNA flow cytometry (FCM) by the EM algorithm. Cytometry 10, 695-705.
3. Blake, R.A. 2007. Target validation in drug discovery. Methods Mol. Biol. 356, 367-377.
4. Cellomics. 2009. Cellomics HCS Reader: Target Activation BioApplication Guide (V2 version). Available at: www.cellomics.com=content=menu=Target- Activation. Accessed November 1, 2009.
5. De Brabander, M., De May, J., Joniau, M., et al. 1977. Ultrastructural immunocytochemical distribution of tubulin in cultured cells treated with microtubule inhibitors. Cell Biol. Int. Rep. 1, 177-183.
6. Durr, O., Duval, F., Nichols, A., et al. 2007. Robust hit identification by quality assurance and multivariate data analysis of a high content cell-based assay. J. Biomol. Screen. 12, 1042-1049.
7. Eudey, T.L. 1996. Statistical considerations in DNA flow cytometry. Statist. Sci. 11, 320-334.
8. Evans, J.G., and Matsudaira, P. 2006. Linking microscopy and high content screening in large-scale biomedical research. Methods Mol. Biol. 356, 33-38.
9. Gasparri, F., Cappella, P., and Galvani, A. 2006. Multiparametric cell cycle analysis by automated microscopy. J. Biomol. Screen. 11, 586-598.
10. Ghosh, R.N., Grove, L., and Lapets, O. 2004. A quantitative cell-based high-content screening assay for the epidermal growth factor receptor-specific activation of mitogen-activated protein kinases. Assay Drug Dev. Technol. 2, 473-481.
11. Hastie, T., Tibshirani, R., and Friedman, J. 2001. The Element of Statistical Learning: Data Mining, Inference and Prediction. Springer, New York.
12. Huang, S. 2007a. On some basic statistical issues in analyzing high-content imaging data (unpublished manuscript).
13. Huang, S., Dowless, M., and Stancato, L. 2007b. Statistical deconvolution of cell populations from high content imaging studies. High Content Analysis 2007. San Francisco.
14. Huang, S., Yeo, A.A., and Li, S.D. 2007c. Modification of Kolmogorov-Smirnov test for DNA content data analysis through distribution alignment. Assay Drug Dev. Technol. 5, 663-671.
15. Huang, P., Chubb, S., Hertel, L.W., et al. 1991. Action of 2',2'-difluorodeoxycytidine on DNA synthesis. Cancer Res. 51, 6110-6117.
16. Lampariello, F. 2000. On the use Kolmogorov-Smirnov statistical test for immunofluorescence histogram comparison. Cytometry 39, 179-188.
17. Loechel, F., Bjorn, S., Linde, V., et al. 2007. High content translocation assays for pathway profiling. Methods Mol. Biol. 356, 401-414.
18. Loo, L.H., Wu, F., and Altschuler, S.J. 2007. Image-based multivariate profiling of drug responses from single cells. Nat. Methods 4, 445-453.
19. Low, J., Huang, S., Blosser, W., et al. 2008. High content imaging characterization of cell cycle therapeutics through in vitro and in vivo subpopulation analysis. Mol. Cancer Ther. 7, 2455-2463.
20. Low, L., Huang, S., Dowless, M., et al. 2007. High-content imaging analysis of the knockdown effects of validated siRNAs and antisense oligonucleotides. J. Biomol. Screen. 12, 775-788.
21. Mann, R.C., Hand, R.E., Jr., and Braslawsky, G.R. 1983. Parametric analysis of histograms measured in flow cytometry. Cytometry 4, 75-82.
22. Nichols, A. 2007. High content screening as a screening tool in drug discovery. Methods Mol. Biol. 356, 379-387.
23. O'Brien, P., and Haskins, J.R. 2007. In vitro cytotoxicity assessment. Methods Mol. Biol. 356, 415-425.
24. Schiff, P.B., and Horwitz, S.B. 1980. Taxol stabilizes microtubules in mouse fibroblast cells. Proc. Natl. Acad. Sci. U.S.A. 77, 1561-1565.
25. Silverman, B.W. 1986. Density Estimation for Statistics and Data Analysis. Chapman and Hall. London.
26. Spadari, S., Pedrali-Noy, G., Focher, F., et al. 1986. DNA polymerases and DNA topoisomerases as targets for the development of anticancer drugs. Anticancer Res. 6, 935-940.
27. Stilwell, J.L., Guan, Y., Neve, R.M., et al. 2007. Systems biology in cancer research. Methods Mol. Biol. 356, 353-365.
28. Taylor, D.L., Haskins, J.R., and Giuliano, K.A. 2007. High Content Screening: A Powerful Approach to Systems Cell Biology and Drug Discovery. Humana Press, Totowa, NJ.
29. Taylor, D.L., and Giuliano, K.A. 2005. Multiplexed high content screening assays create a systems cell biology approach to drug discovery. Drug Discov. Today Technol. 2, 149-154.
30. Taylor, D.L., Woo, E.S., and Giuliano, K.A. 2001. Real-time molecular and cellular analysis: the new frontier of drug discovery. Curr. Opin. Biotechnol. 12, 75-81.
31. Vindelov, L.L., and Christensen, I.J. 1990. A review of techniques and results obtained in one laboratory by an integrated system of methods designed for routing clinical flow cytometric DNA analysis. Cytometry 11, 753-770.
32. Vogt, A., and Lazo, J.S. 2007. Discovery of protein kinase phosphatase inhibitors. Methods Mol. Biol. 356, 389-400.
33. Wang, H., and Huang, S. 2007 Mixture model classification in DNA content analysis. Cytometry A 71A, 716-723.
34. Wilkins, M.R., Appel, R.D., Van Eyk, J.E., et al. 2006. Guidelines for the next 10 years of proteomics. Proteomics 6, 4-8.
35. Young, I.T. 1977. Proof without prejudice: use of the Kolmogorov-Smirnov test for the analysis of histograms from flow systems and other sources. J. Histochem. Cytochem. 25, 935-941.
36. Young, D.W., Bender, A., Hoyt, J., et al. 2008. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat. Chem. Biol. 4, 59-68.