Differential analysis of 2D gel images

Methods in Enzymology

Volumn 487, Issue C, 2011, Pages 595-609

  Li, Feng ^a   Seillier Moiseiwitsch, Françoise ^b  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b Uniformed Services University of the Health Sciences   (United States)

Author keywords

2D gel; 2D PAGE; Differential analysis; Proteomics; Software

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GEL; HUMAN; IMAGE ANALYSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

EID: 78650884354     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381270-4.00021-4     Document Type: Chapter

References (14)

1. Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289-300.
2. Cleveland, W. (1993). A model for studying display methods of statistical graphics. J. Comput. Graph. Stat. 2, 323-364.
3. Conradsen, K., and Pedersen, J. (1992). Analysis of two-dimensional electrophoretic gels. Biometrics 48, 1273-1287.
4. Efron, B. (2007). Correlation and large-scale simultaneous significance testing. J. Am. Stat. Assoc. 102, 93-103.
5. Gonzalez, R., and Woods, R. (2002). Digital Image Processing, Prentice Hall, New York.
6. Li, Feng (2007). Empirical Bayes Methods for Proteomics (Ph.D. Dissertation, University of Maryland, Baltimore County).
7. O'Farrell, P. H. (1975). High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021.
8. Otsu, N. (1979). A threshold selection method from gray level histograms. IEEE Trans. Syst. Man Cybern. 9, 62-66.
9. Potra, F., Liu, X., Seillier-Moiseiwitsch, F., Roy, A., Hang, Y., Marten, M. M., and Raman, B. (2006). Protein image alignment via piecewise afine transformations. J. Comput. Biol. 13, 614-630.
10. Qiu, X., Klebanov, L., and Yakovlev, A. (2005). Correlation between gene expression levels and limitations of the empirical Bayes methodology for finding differentially expressed genes. Stat. Appl. Genet. Mol. Biol. 4, 1-13.
11. Roy, A., Seillier-Moiseiwitsch, F., Lee, K., Hang, Y., Marten, M. M., and Raman, B. (2003). Analyzing two-dimensional gel images. Chance 16, 13-18.
12. Vincent, L., and Soille, P. (1991). Watersheds in digital spaces: An efficient algorithm based on immersion simulations. IEEE Trans. Pattern Anal. Mach. Intell. 13, 583-598.
13. Wilkins, M. R., Pasquali, C., Appel, R. D., Ou, K., Golaz, O., Sanchez, J., Yan, J. X., Gooley, A. A., Hughes, G., Humphery-Smith, I., Williams, K. L., and Hochstrasser, D. F. (1996). From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and arnino acid analysis. Nat. Biotechnol. 14, 61-65.
14. Wilkins, M. R., Appel, R. D., Williams, K. L., and Hochstrasser, D. F. (eds.), (2007). Proteome Research: Concepts, Technology and Application, Springer, Berlin.