On the statistical analysis of the GS-NS0 cell proteome: Imputation, clustering and variability testing

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1764, Issue 7, 2006, Pages 1179-1187

  Ahmad, Norhaiza ^a   Zhang, Jian ^a   Brown, Phillip J ^a   James, David C ^b   Birch, John R ^c   Racher, Andrew J ^c   Smales, C Mark ^a  

^a UNIVERSITY OF KENT   (United Kingdom)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c LONZA AG   (Switzerland)

Author keywords

2D PAGE; hierarchical clustering; imputed values; NS0 cells; proteomic profiling; rank correlation

Indexed keywords

PROTEOME;

ANIMAL CELL; ANTIBODY PRODUCTION; ARTICLE; CALCULATION; CORRELATION ANALYSIS; DATA ANALYSIS; MATHEMATICAL ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; STATISTICAL ANALYSIS;

ALGORITHMS; ANIMALS; ANTIBODIES, MONOCLONAL; CELL LINE, TUMOR; CLUSTER ANALYSIS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GLUTAMATE-AMMONIA LIGASE; IMAGE PROCESSING, COMPUTER-ASSISTED; PRINCIPAL COMPONENT ANALYSIS; PROTEOME; PROTEOMICS; RECOMBINANT PROTEINS;

EID: 33746102132     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2006.05.002     Document Type: Article

References (18)

1. Wasinger V.C., Cordwell S.J., Cerpapoljak A., Yan J.X., Gooley A.A., Wilkins M.R., Duncan M.W., Harris R., Williams K.L., and Humpherysmith I. Progress with gene-product mapping of the mollicutes - mycoplasma-genitalium. Electrophoresis 16 (1995) 1090-1094
2. Lefkovits I., Kettman J.R., and Frey J.R. Global analysis of gene expression in cells of the immune system I. Analytical limitations in obtaining sequence information on polypeptides in two-dimensional gel spots. Electrophoresis 21 (2000) 2688-2693
3. Juan H.F., Lin J.Y., Chang W.H., Wu C.Y., Pan T.L., Tseng M.J., Khoo K.H., and Chen S.T. Biomic study of human myeloid leukemia cells differentiation to macrophages using DNA array, proteomic, and bioinformatic analytical methods. Electrophoresis 23 (2002) 2490-2504
4. Nishihara J.C., and Champion K.M. Quantitative evaluation of proteins in one- and two-dimensional polyacrylamide gels using a fluorescent stain. Electrophoresis 23 (2002) 2203-2215
5. Mahon P., and Dupree P. Quantitative and reproducible two-dimensional gel analysis using Phoretix 2D Full. Electrophoresis 22 (2001) 2075-2085
6. Smales C.M., Birch J.R., Racher A.J., Marshall C.T., and James D.C. Evaluation of individual protein errors in silver-stained two-dimensional gels. Biochem. Biophys. Res. Commun. 306 (2003) 1050-1055
7. Smales C.M., Dinnis D.M., Stansfield S.H., Alete D.E., Sage E.A., Birch J.R., Racher A.J., Marshall C.T., and James D.C. Comparative proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnol. Bioeng. 88 (2004) 474-488
8. Dowsey A.W., Dunn M.J., and Yang G.Z. The role of bioinformatics in two-dimensional gel electrophoresis. Proteomics 3 (2003) 1567-1596
9. Chipman H., Hastie T.J., and Tibshirani R. Clustering Microarray Data, in Statistical Analysis of Gene Expression Microarray Data. In: Speed T. (Ed) (2003), Chapman and Hall, London 159-200
10. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S.A. 95 (1998) 14863-14868
11. Alter O., Brown P.O., and Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 10101-10106
12. Krzanowski W. Principles of Multivariate Analysis: a Users Perspective (1988), Oxford University Press, Oxford
13. Schadt E.E., Li C., Ellis B., and Wong W.H. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell. Biochem., Suppl. 37 (2001) 120-125
14. Taylor J., and Giometti C.S. Use of principal components analysis for mutation detection with two-dimensional electrophoresis protein separations. Electrophoresis 13 (1992) 162-168
15. Storey J.D., and Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 9440-9445
16. Kettman J.R., Robinson R.A., Kuhn L., and Lefkovits I. Global analysis of lymphocyte gene expression: Perturbation of H-9 cells by infection with distinct isolates of human immunodeficiency virus-An exposition by multivariate analysis of a host-parasite interface. Electrophoresis 12 (1991) 554-569
17. Lemkin P.F., and Lester E.P. Database and search techniques for two-dimensional gel protein data: a comparison of paradigms for exploratory data analysis and prospects for biological modelling. Electrophoresis 10 (1989) 122-140
18. Picard P., Bourgoin-Greneche M., and Zivy M. Potential of two-dimensional electrophoresis in routine identification of closely related durum wheat lines. Electrophoresis 18 (1997) 174-181