VizStruct: Exploratory visualization for gene expression profiling

Bioinformatics

Volumn 20, Issue 1, 2004, Pages 85-92

  Zhang, Li ^a   Zhang, Aidong ^a   Ramanathan, Murali ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CLASSIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; DECISION THEORY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MAPPING; GENETIC ALGORITHM; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; VALIDATION PROCESS;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER GRAPHICS; FEMALE; GENE EXPRESSION; GENETIC SCREENING; HUMANS; MALE; MULTIPLE SCLEROSIS; NEOPLASMS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SIGNAL PROCESSING, COMPUTER-ASSISTED; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 0346463227     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg377     Document Type: Article

References (24)

1. Alizadeh,A.A., Eisen,M.B., Davis,R.E., Ma,C., Lossos,I.S., Rosenwald,A., Boldrick,J.C., Sabet,H., Tran,T., Yu,X., et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403, 503-511.
2. Alon,U., Barkai,N., Notterman,D.A., Gish,K., Ybarra,S., Mack,D. and Levine,A.J. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide array. Proc. Natl Acad. Sci. USA, 96, 6745-6750.
3. Bellman,R. (1961) Adaptive Control Processes: A Guided Tour. Princeton University Press, Princeton, NJ.
4. Cadzow,J.A. and Landingham,H.F. (1985) Signals, Systems, and Transforms. Prentice-Hall, Inc., Englewood Cliffs, NJ.
5. Cohen,J. (1960) A coefficient of agreement for nominal scales. Ed. & Psych. Meas., 20, 37-46.
6. Cook,C., Buja,A., Cabrera,J. et al. (1995) Grand tour and projection pursuit. J. Comput. Graph. Stat., 2, 225-250.
7. Cooley,J.W. and Tukey,J.W. (1965) An Algorithm for the machine calculation of complex Fourier series. Math. Comput., 19, 297-301.
8. Eisen,M.B., Spellman,P.T., Brown,P.O. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
9. Ewing,R.M. and Cherry,J.M. (2001) Visualization of expression clusters using Sammon's non-linear mapping. Bioinformatics, 17, 658-659.
10. Fisher,R.A. (1936) The use of multiple measurements on taxonomic problems. Ann. Eugenics, 7, 179-188.
11. Golub,T.R., Slonim,D.K., Tamayo,P., Huard,C., Gassenbeek,M., Mesirov,J.P., Coller,H., Loh,M.L., Downing,J.R., Caligiuri,M.A. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
12. Hautaniemi,S., Yli-Huja,O., Astola,J. et al. (2003) Analysis and visualization of gene expression microarray data in human cancer using self-organizing maps. Machine Learning: Special Issue on Methods in Functional Genomics (To appear).
13. Hedenfalk,I., Duggan,D., Chen,Y., Radmacher,M., Bittner,M., Simon,R., Meltzer,P., Gusterson,B., Esteller,M., Kallioniemi,O.P. et al. (2001) Gene-expression profiles in hereditary breast cancer. N. Eng. J. Med., 344, 539-548.
14. Hoffman,P.E., Grinstein,G.G., Marx,K., Grosse,I. and Stanley,E. (1997) DNA visual and analytic data mining. IEEE Visualization'97, Phoenix, AZ, 437-441.
15. Khan,J., Wei,J.S., Ringnér,M., Saal,L.H., Ladanyi,M., Westermann,F., Berthold,F., Schwab,M., Antonescu,C.R., Peterson,C. et al. (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med., 7, 673-679.
16. Kohonen,T. (1995) Self-Organizing Maps, Springer Series in Information Sciences, Vol. 30. Springer, Berlin, Heidelberg, New York.
17. Landis,J. and Koch,G.G. (1977) The measurement of observer agreement for categorical data. Biometrics, 33, 159-174.
18. Morrison,N. (1994) Introduction to Fourier Analysis. John Wiley & Sons, Inc., New York, NY.
19. Murthy,S.K., Kasif,S., Salzberg,S. and Beigel,R. (1993) OC1: a randomized induction of oblique decision trees. National Conference on Artificial Intelligence. Washington, DC, pp. 322-327.
20. Murthy,S.K., Kasif,S. and Salzberg,S. (1994) A system for induction of oblique decision trees. J. Art. Intell. Res., 2, 1-32.
21. Sammon,J.W. (1969) A nonlinear mapping for data structure analysis. IEEE Trans. Comp., C-18, 401-409.
22. Tusher,V.G., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121.
23. Virtaneva,K., Wright,F., Tanner,S. et al. (2001) Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetic. Proc. Natl Acad. Sci. USA, 98, 1124-1129.
24. Zhang,L., Tang,C., Song,Y.Q., Zhang,A., and Ramanathan,M. (2003) VizCluster and its application on clustering gene expression data. Int. J. Distributed and Parallel Databases, 13, 79-97.