Graphical Exploration of Gene Expression Data: A Comparative Study of Three Multivariate Methods

Biometrics

Volumn 59, Issue 4, 2003, Pages 1131-1139

  Wouters, Luc ^a   Göhlmann, Hinrich W ^b   Bijnens, Luc ^b   Kass, Stefan U ^b   Molenberghs, Geert ^a   Lewi, Paul J ^b  

^a HASSELT UNIVERSITY   (Belgium)

^b JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

Author keywords

Bioinformatics; Biplot; Correspondence factor analysis; Data mining; Data visualization; Gene expression data; Microarray data; Multivariate exploratory data analysis; Principal component analysis; Spectral map analysis

Indexed keywords

DATA HANDLING; DATA VISUALIZATION; FACTOR ANALYSIS; GENE EXPRESSION; MULTIVARIANT ANALYSIS; PRINCIPAL COMPONENT ANALYSIS;

BIPLOTS; CORRESPONDENCE FACTOR ANALYSIS; EXPLORATORY DATA ANALYSIS; GENE EXPRESSION DATA; MAP ANALYSIS; MICROARRAYS DATA; MULTIVARIATE EXPLORATORY DATA ANALYSE; PRINCIPAL-COMPONENT ANALYSIS; SPECTRAL MAP ANALYSE; SPECTRAL MAPS;

DATA MINING;

GENE EXPRESSION;

BIOINFORMATICS; COMPARATIVE STUDY; DNA MICROARRAY; GENE EXPRESSION; HUMAN; LEUKEMIA; PRINCIPAL COMPONENT ANALYSIS; RELIABILITY; REVIEW;

CELL FUSING AGENT VIRUS;

EID: 0347994074     PISSN: 0006341X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0006-341X.2003.00130.x     Document Type: Review

References (23)

1. Andries, K., Dewindt, B., Snoeks, J., Wouters, L., Moereels, H., Lewi, P. J., and Janssen, P. A. J. (1990). Two groups of rhinoviruses revealed by a panel of antiviral compounds present sequence divergence and differential pathogenicity. Journal of Virology 64, 1117-1123.
2. Benzécri, J. P. (1973). L'analyse des données, Volume II: L'Analyse des Correspondences. Paris: Gounod.
3. Chapman, S., Schenk, P., Kazan, K., and Manners, J. (2001). Using biplots to interpret gene expression patterns in plants. Bioinformatics 18, 202-204.
4. Chow, M. L., Moler, E. J., and Mian, I. S. (2001). Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiological Genomics 5, 99-11.
5. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences U.S.A. 95, 14863-14868.
6. Faes, W. and Lewi, P. J. (1987). Spectramap: The story behind your numbers. International Management Development Review 3, 183-187.
7. Fellenberg, K., Hauser, N., Brors, B., Neutzner, A., Hoheisel, J., and Vingron, M. (2001). Correspondence analysis applied to microarray data. Proceedings of the National Academy of Sciences U.S.A. 98, 10781-10786.
8. Gabriel, K. R. (1971). The biplot graphical display of matrices with applications to principal component analysis. Biometrika 58, 453-467.
9. Golub, T. R., Slonim, D. K., Tamayo, P., et al (1999). Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286, 531-537.
10. Greenacre, M. J. (1984). Theory and Applications of Correspondence Analysis. London: Academic Press.
11. Hermy, M. and Lewi, P. J. (1991). Multivariate ratio analysis, a graphic method for ecological ordination. Ecology 72, 735-738.
12. Hilsenbeck, S. G., Friedrichs, W. E., Schiff, R., O'Connell, P., Hansen, R. K., Osborne, C. K., and Fuqua, S. A. (1999). Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. Journal of the National Cancer Institute 91, 453-459.
13. Hotelling, H. (1933). Analysis of a complex of statistical variables into principal components. Journal of Educational Psychology 24, 417-441.
14. Landgrebe, J., Welzl, G., Metz, T., van Gaalen, M. M., Ropers, H., Wurst, W., and Holsboer, F. (2002). Molecular characterisation of antidepressant effects in the mouse brain using gene expression profiling. Journal of Psychiatric Research 36, 119-129.
15. Lefkovits, I., Kuhn, L., Valiron, O., Merle, A., and Kettman, J. (1988). Toward an objective classification of cells in the immune system Proceedings of the National Academy of Sciences U.S.A. 85, 3565-3569.
16. Lewi, P. J. (1976). Spectral mapping, a technique for classifying biological activity profiles of chemical compounds. Arzneimittel Forschung (Drug Research) 26, 1295-1300.
17. Lewi, P. J. and Moereels, R. (1994). Receptor mapping and phylogenetic clustering. In Advanced Computer-Assisted Techniques of Drug Discovery, H. van de Waterbeemd (ed), 131-162. Weinheim, Germany: VCH.
18. Pearson, K. (1901). On lines and planes of closest fit to points in space. Philosophical Magazine 2, 559-572.
19. Rancano, C., Rubio, T., Correas, I., and Alonso, M. A. (1994). Genomic structure and subcellular localization of MAL, a human T-cell-specific proteolipid protein. Journal of Biological Chemistry 269, 8159-8164.
20. Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J., and Church, G. M. (1999). Systematic determination of genetic network architecture. Nature Genetics 22, 281-285.
21. Thielemans, A., Lewi, P. J., and Massart, D. L. (1988). Similarities and differences among multivariate display techniques illustrated by Belgian cancer mortality distribution data. Chemometrics and Intelligent Laboratory Systems 3, 277-300.
22. Törönen, P., Kolehmainen, M., Wong, G., and Castrén, E. (1999). Analysis of gene expression data using self-organizing maps. FEBS Letters 451, 142-146.
23. Virgilio, L., Narducci, M. G., Isobe, M., Billips, L. G., Cooper, M. D., Croce, C. M., and Russo, G. (1994). Identification of the TCL1 gene involved in T-cell malignancies. Proceedings of the National Academy of Sciences U.S.A. 91, 12530-12534.