Influence of microarray experiments missing values on the stability of gene groups by hierarchical clustering

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  de Brevern, Alexandre G ^a   Hazout, Serge ^a   Malpertuy, Alain ^b  

^a INSERM   (France)

^b Atragene Bioinformatics   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AGGREGATION ALGORITHMS; HIER-ARCHICAL CLUSTERING; HIERARCHICAL CLUSTERING ALGORITHMS; K NEAREST NEIGHBOR (KNN); MICROARRAY DATA SETS; MICROARRAY EXPERIMENTS; MICROARRAY TECHNOLOGIES; STATISTICAL TREATMENT;

CLUSTERING ALGORITHMS; EXPERIMENTS; MICROARRAYS; STABILITY; TEXT PROCESSING;

GENE EXPRESSION;

DNA;

ALGORITHM; ANALYTIC METHOD; ANALYTICAL ERROR; ANALYTICAL PARAMETERS; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION; GENE LOCATION; GENETIC LINKAGE; GENETIC STABILITY; HUMAN; INTERMETHOD COMPARISON; NEIGHBOR JOINING METHOD; NONHUMAN; SACCHAROMYCES CEREVISIAE; SENSITIVITY ANALYSIS; STATISTICAL ANALYSIS; BIOLOGY; FUNGAL GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; METHODOLOGY; PROCEDURES; REFERENCE VALUE; STATISTICS AND NUMERICAL DATA;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REFERENCE VALUES; RESEARCH DESIGN; SACCHAROMYCES CEREVISIAE;

EID: 13244278004     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-114     Document Type: Article

References (37)

1. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control gene expression on a genomic scale. Science 1997, 278:680-686.
2. Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ: Genomewide mapping with biallelic markers in Arabidopsis thaliana. Nature Genet 2003, 23:203-207.
3. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J: Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 2003, 13:513-523.
4. Liu CH, Ma WL, Shi R, Ou YQ, Zhang B, Zheng WL: Possibility of using DNA chip technology for diagnosis of human papillomavirus. J Biochem Mol Biol 2003, 36:349-353.
5. Locke DP, Segraves R, Carbone L, Archidiacono N, Albertson DG, Pinkel D, Eichler EE: Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res 2003, 13:347-357.
6. Everitt B: Cluster Analysis,. Heinemann Educ 1974.
7. Hartigan JA, Wong MA: A k-means clustering algorithm,. Applied Statistics 1979, 28:100-108.
8. Kohonen T: Self-organized formation of topologically correct feature maps. Biol Cybern 1982, 43:59-69.
9. Kohonen T: Self-Organizing Maps,. 3rd edition. Springer Verlag; 2001.
10. Mardia KV, Kent JT, Bibby JM: Multivariate Analysis. Academic Press; 1979.
11. Lee S-I, Batzogolou S: Application of Independent Component Analysis to microarrays. Genome Biology 2003, 4: 76.
12. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
13. Quackenbush J: Computational analysis of microarray data. Nature genetics 2001, 418:418-427.
14. Yeung KY, Haynor DR, Ruzzo WL: Validating clustering for gene expression data. Bioinformatics 2001, 17:309-318.
15. Gibbons FD, Roth FP: Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res 2002, 12:1574-1581.
16. Schuchhardt J, Beule A, Malik A, Wolski H, Eickoff H, Lehrarch H, Herzel H: Normalization strategies for cDNA microarrays. Nucl Acids Res 2000, 28:E47.
17. Tu Y, Stolovitzky G, Klein U: Quantitative noise analysis for gene expression microarray experiments. Proc Natl Acad Sci USA 2002, 99:14031-14036.
18. Troyanskaya OG, Cantor M, Sherlock G, Brown PO, Hastie T, Tibshirani R, Botstein D, Altman RB: Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17:520-525.
19. Oba S, Sato M-A, Takemasa I, Monden M, Matsubara K-I, Ishii S: A Bayesian missing value estimation method for gene expression profile data,.Bioinformatics 2003, 19:2088-2096.
20. Zhou X, Wang X, Dougherty ER: Missing-value estimation using linear and non-linear regression with Bayesian gene selection. Bioinformatics 2003, 19:2302-2307.
21. Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R: Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci USA 2003, 100:1926-1930.
22. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lonning PE, Brown PO, Borresen-Dale AL, Botstein D: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003, 100:8418-8423.
23. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I: Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 2001, 98:13784-13789.
24. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
25. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11:4241-4257.
26. 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.
27. Ferea TL, Botstein D, Brown PO, Rosenzweig RF: Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci USA 1999, 96:9721-9726.
28. 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.
29. Liu L, Hawkins DM, Ghosh S, Young SS: Robust singular value decomposition analysis of microarray data. Proc Natl Acad Sci USA 2003, 100:13167-13172.
30. Tilstone C: Vital Statistics. Nature 2003, 424:610-612.
31. Yeung KY, Medvedovic M, Bumgarner RE: Clustering gene-expression data with repeated measurements. Genome Biology 2003, 4:R34.
32. Nikkilä J, Törönen P, Kaski S, Venna J, Castren E, Wong G: Analysis and visualization of gene expression data using Self-Organizing Maps. Neural Networks 2002, 15:953-966.
33. Herrero J, Valencia A, Dopazo J: A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 2001, 17:126-136.
34. Herrero J, Dopazo J: Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns. J Proteome Res 2002, 1:467-470.
35. Hsu A, Tang SL, Halgamuge S: An unsupervised hierarchical dynamic self-organising approach to cancer class discovery and marker gene identification in microarray data. Bioinformatics 2003, 19:2131-2140.
36. Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G: The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res 2003, 31:94-96.
37. Ihaka R, Gentleman R: A Language for Data Analysis and Graphics. J Comput Graph Stat 1996, 5:299-314.