The theoretic framework of local weighted approximation for microarray missing value estimation

Pattern Recognition

Volumn 43, Issue 8, 2010, Pages 2993-3002

  Liu, Chao Chun ^a,b   Dai, Dao Qing ^a   Yan, Hong ^b,c  

^a Department of Mathematics   (China)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF SYDNEY   (Australia)

Author keywords

DNA microarray data analysis; Local weighted approximation; Missing value estimation

Indexed keywords

BIOMEDICAL EXPERIMENTS; DATA IMPUTATION; DNA MICROARRAY DATA; GLOBAL INFORMATIONS; IMPUTATION ALGORITHM; IMPUTATION METHODS; K-NEAREST NEIGHBORS; LINEAR APPROXIMATIONS; MICROARRAY DATA; MISSING VALUE ESTIMATION; MISSING VALUES; STATISTICAL ALGORITHM; TAYLOR SERIES APPROXIMATION; WEIGHTED APPROXIMATION;

AUTOCORRELATION; DNA; ESTIMATION; EXPERIMENTS; GENES;

DATA HANDLING;

EID: 77951253977     PISSN: 00313203     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.patcog.2010.02.006     Document Type: Article

References (32)

1. Lockhart D.J., and Winzeler E.A. Genomics, gene expression and DNA arrays. Nature 405 (2000) 827-836
2. Schulze A., and Downward J. Navigating gene expression using microarrays-a technology review. Nature cell biology 3 (2001) E190-E195
3. Perou C.M., Sørlie T., Eisen M.B., et al. Molecular portraits of human breast tumours. Nature 406 (2000) 747-752
4. Chu S., DeRisi J., Eisen M., et al. The transcriptional program of sporulation in budding yeast. Science 282 (1998) 699-705
5. Liewa A.W.C., Yan H., and Yang M.S. Pattern recognition techniques for the emerging field of bioinformatics: a review. Pattern Recognition 38 11 (2005) 2055-2073
6. Lin T.C., Liu R.S., Chen C.Y., Chao Y.T., and Chen S.Y. Pattern classification in DNA microarray data of multiple tumor types. Pattern Recognition 39 12 (2006) 2426-2438
7. Pugazhenthi D., and Rajagopalan S.P. Machine learning technique approaches in drug discovery, design and development. Information Technology Journal 6 5 (2007) 718-724
8. Joung J.G., O S.J., and Zhang B.T. Protein sequence-based risk classification for human papillomaviruses. Computers in Biology and Medicine 36 (2006) 656-667
9. Tuikkala J., Elo L.L., Nevalainen O.S., and Aittokallio T. Missing value imputation improves clustering and interpretation of gene expression microarray data. BMC Bioinformatics 9 202 (2008)
10. Farhangfar A., Kurgan L., and Dy J. Impact of imputation of missing values on classification error for discrete data. Pattern Recognition 41 12 (2008) 3692-3705
11. Ouyang M., Welsh W.J., and Georgopoulos P. Gaussian mixture clustering and imputation of microarray data. Bioinformatics 20 (2004) 917-923
12. Y.H. Yang, M.J. Buckley, S. Dudoit, T.P. Speed, Comparison of methods for image analysis in cDNA microarray data, Technical Report 584, Department of Statistics, UC, Berkeley, 2000.
13. Troyanskayaet O., Cantor M., Sherlock G., et al. Missing value estimation methods for DNA microarrays. Bioinformatics 17 6 (2001) 520-525
14. Tuikkala J., Elo L., Nevalainen O.S., and Aittokallio T. Improving missing value estimation in microarray data with gene ontology. Bioinformatics 22 (2006) 566-572
15. Xiang Q., Dai X.H., Deng Y.Y., et al. Missing value imputation for microarray gene expression data using histone acetylation information. BMC Bioinformatics 9 252 (2008)
16. Oba S., Sato M.A., Takemasa I., et al. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 19 (2003) 2088-2096
17. Kim H., Golub G.H., and Park H. Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics 21 (2005) 187-198
18. Bø T.H., Dysvik B., and Jonassen I. Lsimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Research 32 3 (2004)
19. Yoon D., Lee E.K., and Park T. Robust imputation method for missing values in microarray data. BMC Bioinformatics 8 2 (2007)
20. Sehgal M.S.B., Gondal I., and Dooley L.S. Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data. Bioinformatics 21 (2005) 2417-2423
21. Gan X.C., Liew A.W.C., and Yan H. Microarray missing data imputation based on a set theoretic framework and biological knowledge. Nucleic Acids Research 34 5 (2006)
22. Jornsten R., Wang H.Y., Welsh W.J., and Ouyang M. DNA microarray data imputation and significance analysis of differential expression. Bioinformatics 21 (2005) 4155-4161
23. Choong M.K., Charbit M., and Yan H. Autoregressive-model-based missing value estimation for DNA microarray time series data. IEEE Transaction on Information Technology in Biomedicine 13 (2009) 131-137
24. Fan J.Q. Design-adaptive nonparametric regression. Journal of the American Statistical Association 87 420 (1992) 998-1004
25. Fan J.Q. Local linear regression smoothers and their minimax efficiencies. Annals of Statistics 21 1 (1993) 196-216
26. Spellman P.T., Sherlock G., Zhang M.Q., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9 (1998) 3273-3297
27. DeRisi J.L., Iyer V.R., and Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278 (1997) 680-686
28. Gasch A.P., Spellman P.T., Kao C.M., et al. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11 (2000) 4241-4257
29. +-dependent deacetylases using phenotypic screens in yeast. Journal of Biological Chemistry 278 (2003) 52773-52782
30. Alizadeh A.A., Eisen M.B., Davis R.E., and Ma C. Distinct types of diffuse large B-cell lymphoma identified by gene-expression profiling. Nature 403 (2000) 503-511
31. Ronen M., and Botstein D. Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. PNAS 103 (2005) 389-394
32. Brock G.N., Shaffer J.R., Blakesley R.E., Lotz M.J., and Tseng G.C. Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes. BMC Bioinformatics 9 12 (2008)