Integrative missing value estimation for microarray data

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Hu, Jianjun ^a   Li, Haifeng ^a   Waterman, Michael S ^a   Zhou, Xianghong Jasmine ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMPUTATION ALGORITHM; LOCAL LEAST SQUARES; MICRO-ARRAY DATABASE; MICROARRAY ANALYSIS; MICROARRAY DATA SETS; MISSING VALUE ESTIMATION; MULTIPLE REFERENCES; PRE-PROCESSING STEP;

BENCHMARKING; DATA REDUCTION; GENES;

ESTIMATION;

ACCURACY; ALGORITHM; ARTICLE; DNA MICROARRAY; MEASUREMENT; NOISE; QUALITY CONTROL; SAMPLE (STATISTICS); STANDARD; STATISTICAL ANALYSIS; BIOLOGICAL MODEL; COMPUTER SIMULATION; DATA BASE; GENE EXPRESSION PROFILING; GENETIC DATABASE; INFORMATION RETRIEVAL; PROBABILITY; PROCEDURES; PROTEIN DATABASE; SAMPLE SIZE; STATISTICAL MODEL; SYSTEM ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SAMPLE SIZE; SYSTEMS INTEGRATION;

EID: 33750386831     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-449     Document Type: Article

References (24)

1. Hoheisel JD: Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet 2006, 7:200-210.
2. de Brevern AG, Hazout S, Malpertuy A: Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. BMC Bioinformatics 2004, 5:114.
3. Bo TH, Dysvik B, Jonassen I: LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Res 2004, 32:e34.
4. Kim H, Golub GH, Park H: Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics 2005, 21:187-198.
5. M. Scholz, F. Kaplan, C.L. Guy, J. Kopka, J. Selbig: Non-linear PCA: a missing data approach. In Bioinformatics Volume 21. Oxford; 2005:3887-3895.
6. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB: Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17:520-525.
7. Zhou X, Wang X, Dougherty ER: Missing-value estimation using linear and non-linear regression with Bayesian gene selection. Bioinformatics 2003, 19:2302-2307.
8. Oba S, Sato MA, Takemasa I, Monden M, Matsubara K, Ishii S: A Bayesian missing value estimation method for gene expression profile data. Bioinformatics; 2003, 19:2088-2096.
9. Sehgal MS, Gondal I, Dooley LS: Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data. Bioinformatics 2005, 21:2417-2423.
10. Wang X, Li A, Jiang Z, Feng H: Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme. BMC Bioinformatics 2006, 7:32.
11. Ouyang M, Welsh, WJ, Georgopoulos P: Gaussian mixture clustering and imputation of microaarray data. Bioinformatics 2004, 20:917-923.
12. Jornsten R, Wang HY, Welsh WJ, Ouyang M: DNA microarray data imputation and significance analysis of differential expression. Bioinformatics 2005, 21:4155-4161.
13. Tuikkala J, Elo L, Nevalainen OS, Aittokallio T: Improving missing value estimation in microarray data with gene ontology. Bioinformatics 2006, 22:566-572.
14. Princeton SGD Lite yeast datasets 2005 [http://sgdlite.princeton.edu/ download/yeast_datasets/].
15. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
16. Ogawa N, DeRisi J, Brown PO: New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 2000, 11:4309-4321.
17. Ferea TL, Botstein D, Brown PO, Rosenzweig RF: Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 1999, 96:9721-9726.
18. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
19. Zhou XJ, Kao MC, Huang H, Wong A, Nunez-Iglesias J, Primig M, Aparicio OM, Finch CE, Morgan TE, Wong WH: Functional annotation and network reconstruction through cross-platform integration of microarray data. Nat Biotechnol 2005, 23:238-243.
20. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM: Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002, 62:4427-4433.
21. Choi JK, Yu U, Kim S, Yoo OJ: Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 2003, 19:184-190.
22. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Barrette TR, Ghosh D, Chinnaiyan AM: Mining for regulatory programs in the cancer transcriptome. Nat Genet 2005, 37:579-583.
23. Lamb J RSFHLCBMRVKFSZCAPNGTREME: A mechanism of cyclin DI action encoded in the patterns of gene expression in human cancer. Cell 2003, 114:323-334.
24. Stuart JM, Segal E, Koller D, Kim SK: A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.