Multiclass discovery in array data

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Liu, Yingchun ^a   Ringnér, Markus ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BREAST CANCER; DISCRIMINATORY GENE; EXPRESSION LEVELS; MICROARRAY DATA; MICROARRAY DATA SETS; MICROARRAY EXPERIMENTS; RANDOM CLASS; UNSUPERVISED CLASSIFICATION;

EXPERIMENTS; TUMORS;

GENE EXPRESSION;

ACCURACY; ARTICLE; BREAST CANCER; BURKITT LYMPHOMA; CANCER CLASSIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA MICROARRAY; EWING SARCOMA; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC IDENTIFICATION; NEUROBLASTOMA; PREDICTION; QUALITY CONTROL; RANK SUM TEST; RHABDOMYOSARCOMA; TUMOR CELL; BREAST TUMOR; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HUMAN; STATISTICS AND NUMERICAL DATA; TUMOR GENE;

BREAST NEOPLASMS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; SOFTWARE VALIDATION;

EID: 13244292283     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-70     Document Type: Article

References (26)

1. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ED: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286: 31-537.
2. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Wilfond B, Borg A, Trent J: Gene-expression profiles in hereditary breast cancer. N Engl J Med 2001, 344:539-548.
3. Ringnér M, Peterson C, Khan J: Analyzing array data using supervised methods. Pharmacogenomics 2002, 3: 03-415.
4. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, Sampas N, Dougherty E, Wang E, Marincola F, Gooden C, Lueders J, Glatfelter A, Pollock P, Carpten J, Gillanders E, Leja D, Dietrich K, Beaudry C, Berens M, Alberts D, Sondak V, Hayward N, Trent J: Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 2000, 406: 36-540.
5. Sokal RR, Michener CD: A statistical method for evaluating systematic relationships. Univ Kans Sci Bull 1958, 38: 409-1438.
6. Hartigan JA, Wong MA: A K-means clustering algorithm. Applied Statistics 1979, 28:100-108.
7. Kohonen T: Self-Organizing Maps 3rd edition. Berlin: Springer; 2001.
8. Quackenbush J: Computational analysis of microarray data. Nat Rev Genet 2001, 2:418-427.
9. 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 Jr, 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.
10. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D: Molecular portraits of human breast tumours. Nature 2000, 406:747-752.
11. Dugas M, Merk S, Breit S, Dirschedl P: Mdclust - Exploratory microarray analysis by multidimensional clustering. Bioinformatics 2004, 20:931-936.
12. Covell DG, Wallqvist A, Rabow AA, Thanki N: Molecular classification of cancer: unsupervised self-organizing map analysis of gene expression microarray data. Mol Cancer Ther 2003, 2: 17-332.
13. Hsu AL, Tang SL, Halgamuge SK: An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data. Bioinformatics 2003, 19:2131-2140.
14. Ben-Dor A, Friedman N, Yakhini Z: Class discovery in gene expression data. In Proceedings of the Fifth Annual Conference on Computational Biology (RECOMB): 2001; Montreal Edited by: Lengauer T, Sankoff D, Istrail S, Pevzner P, Waterman M. ACM Press; 2001:31-38.
15. von Heydebreck A, Huber W, Poustka A, Vingron M: Identifying splits with clear separation: a new class discovery method for gene expression data. Bioinformatics 2001, 17(Suppl 1 : 107-114.
16. Hedenfalk I, Ringnér M, Ben-Dor A, Yakhini Z, Chen Y, Chebil G, Ach R, Loman N, Olsson H, Meltzer P, Borg Å, Trent J: Molecular classification of familial non-BRCA1/BRCA2 breast cancer. Proc Natl Acad Sci USA 2003, 100:2532-2537.
17. Kirkpatrick S, Gelatt C, Vecchi M: Optimization by simulated annealing. Science 1983, 220:671-680.
18. Ben-Dor A, Bruhn L, Friedman N, Nachman I, Schummer M, Yakhini Z: Tissue classification with gene expression profiles. J Comput Biol 2000, 7:559-583.
19. Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB: Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 2002, 18:1454-1461
20. Khan J, Wei JS, Ringnér M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Atonescu CR, Peterson C, Meltzer PS: Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 2001, 7: 73-679.
21. Wilcoxon F: Individual comparisons by ranking methods. Biometrics 1945, 1:80-83.
22. Walpole RE, Myers RH: Probability and Statistics for Engineers and Scientists 3rd edition. New York: Macmillan; 1985.
23. Kruskal WH, Wallis WA: Use of ranks in one-criterion variance analysis. J Amer Statist Assoc 1952, 47:583-621.
24. Press WH, Teukolsky SA, Vetterling WT, Flannery BP: Numerical Recipes in C 2nd edition. Cambridge, UK: Cambridge University Press; 1992.
25. Ringnér M, Edén, Johansson P: Classification of expression patterns using artificial neural networks. In A Practical Approach to Microarray Data Analysis Edited by: Berrar DP, Dubitzky W, Granzow M. Boston: Kluwer Academic Publishers; 2002:201-215.
26. Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg Å, Peterson C: Bioarray software environment: a platform for comprehensive management and analysis of microarray data. Genome Biol 2002, 3:software0003.1-0003.6.