Dealing with gene expression missing data

IEE Proceedings: Systems Biology

Volumn 153, Issue 3, 2006, Pages 105-119

  Bras L P ^a   Menezes, J C ^a  

^a UNIVERSITY OF LISBON   (Portugal)

Author keywords

A0250; A0260; A8715B; A8725F

Indexed keywords

ARRAYS; ESTIMATION; ITERATIVE METHODS; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS;

GENE EXPRESSION; MICROARRAY DATA; MISSING DATA; MISSING VALUES;

GENES;

ACCURACY; ANALYTICAL ERROR; ANALYTICAL PARAMETERS; ARTICLE; BAYES THEOREM; CONTROLLED STUDY; DATA ANALYSIS; EXPERIMENTAL DESIGN; GENE EXPRESSION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC SIMILARITY; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; TIME SERIES ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SAMPLE SIZE;

EID: 33747418958     PISSN: 17412471     EISSN: None     Source Type: Journal    
DOI: 10.1049/ip-syb:20050056     Document Type: Article

References (33)

1. Watson, A., Mazumder, A., Stewart, M., and Balasubramanian, S. 'Technology for microarray analysis of gene expression', Curr. Opin. Biotechnol., 1998, 9, p. 609-614
2. Duggan, D.J., Bittner, M., Chen, Y., Meltzer, P., and Trent, J.M. 'Expression profiling using cDNA microarrays', Nat. Genet., 1999, 21, p. S10-S14
3. Lockhart, D.J., and Winzeler, E.A. 'Genomics, gene expression and DNA arrays', Nature, 2000, 405, p. 827-836 0028-0836
4. Schulze, A., and Downward, J. 'Navigating gene expression using microarrays - a technology review', Nat. Cell Biol., 2001, 3, p. E190-E195
5. Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. 'Quantitative monitoring of gene expression patterns with a complementary DNA microarray', Science, 1995, 270, p. 467-470 0036-8075
6. Brazma, A., and Vilo, J. 'Gene expression data analysis', FEBS Lett., 2000, 480, p. 17-24
7. Quackenbush, J. 'Computational analysis of microarray data', Nat. Rev. Genet., 2001, 2, p. 418-427
8. Butte, A.: 'The use and analysis of microarray data', Nat. Rev. Drug Discov., 2002, 1, (12), p. 951-960
9. Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Lossos, I.S., Rosenwald, A., Boldrick, J., Sabet, H., Tran, T., and Yu, X.: Et al. 'Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling', Nature, 2000, 403, p. 503-511 0028-0836
10. de Brevern, A.G., Hazout, S., and Malpertuy, A.: 'Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering', BMC Bioinf., 2004, 5, p. 114
11. Schafer, J.L., and Graham, J.W. 'Missing data: Our view of the state of the art', Psychol. Methods, 2002, 7, (2), p. 147-177
12. Little, R.J.A., and Rubin, D.B.: 'Statistical analysis with missing data', (J. Wiley & Sons, New York 1987)
13. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R.B.: 'Missing value estimation methods for DNA microarrays', Bioinformatics, 2001, 17, (6), p. 520-525
14. Kim, K.Y., Kim, B.J., and Yi, G.S. 'Reuse of imputed data in microarray analysis increases imputation efficiency', BMC Bioinf., 2004, 5, p. 160
15. Oba, S., Sato, M.A., Takemasa, I., Monden, M., Matsubara, K., and Ishii, S. 'A Bayesian missing value estimation method for gene expression profile data', Bioinformatics, 2003, 19, (16), p. 2088-2096
16. Kim, H., Golub, G.H., and Park, H. 'Missing value estimation for DNA microarray expression data: Local least squares imputation', Bioinformatics, 2005, 21, p. 187-198
17. Nguyen, D.V., Wang, N., and Carroll, R.J. 'Evaluation of missing value estimation for microarray data', J. Data Sci., 2004, 2, p. 347-370
18. Manly, B.F.J. 'Multivariate statistical methods: A primer', 2nd (Chapman and Hall, London, UK 1998)
19. Jobson, J.D. 'Applied multivariate data analysis: Regression and experimental design', 1st (Springer Verlag, New York 1991), 1,
20. Miller, A.J. 'Subset selection in regression', (Chapman and Hall, London 1990)
21. Helland, I.: 'On the structure of partial least squares', Commun. Stat. Simul. Comput., 1988, 17, p. 581-607 0361-0918
22. Denham, M.C. 'Prediction intervals in partial least squares', J. Chemometr, 1997, 11, (1), p. 39-52
23. Dayal, B.S., and MacGregor, J.F. 'Improved PLS algorithms', J. Chemometr, 1997, 11, p. 73-85
24. Arteaga, F., and Ferrer, A.: 'Sealing with missing data in MSPC: several methods, different interpretations, some examples', J. Chemometr, 2002, 16, (8-10), p. 408-418
25. Denham, M.C.: 'Choosing the number of factors in partial least squares regression: Estimating and minimizing the mean squared error of prediction', J. Chemometr, 2000, 14, (4), p. 351-361
26. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., and Futcher, B. 'Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization', Mol. Biol. Cell., 1998, 9, (12), p. 3273-3297
27. Yoshimoto, H., Saltsman, K., Gasch, A.P., Li, H.X., Ogawa, N., Botstein, D., Brown, P.O., and Cyert, M.S. 'Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae', J. Biol. Chem., 2002, 277, (34), p. 31079-31088
28. Ross, D.T., Scherf, U., Eisen, M.B., Perou, C.M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S.S., Van de Rijn, M., and Waltham, M.: Et al. 'Systematic variation in gene expression patterns in human cancer cell lines', Nat. Genet., 2000, 24, p. 227-235
29. 'The R project for statistical computing', 2004 December), http://www.r-project.org/
30. Hastie, T., Tibshirani, R., Narasimhan, B., and Chu, G. 'Impute: imputation for microarray data ' http://www.bioconductor.org
31. Siegel, S., and Castellan, N.J. 'Nonparametric statistics for behavioral sciences', 2nd (McGraw-Hill, Inc., New York, USA 1988)
32. Levene, H.: 'Robust tests for the equality of variance', Olkin, I., Ghurye, S.G., Hoefding, W., Madow, W., Mann, H.B., Contributions to probability statistics: Essays in honor of Harold Hotelling, (Stanford University Press, Palo Alto, CA, USA 1960), p. 278-292
33. Manly, B.F.J. 'Randomization, bootstrap and Monte Carlo methods in biology', 2nd (Chapman and Hall, London, UK 1997)