Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps

Journal of Biomedical Informatics

Volumn 40, Issue 2, 2007, Pages 160-173

  Brameier, Markus ^a,b   Wiuf, Carsten ^a,b  

^a AARHUS UNIVERSITY   (Denmark)

^b AARHUS UNIVERSITY HOSPITAL   (Denmark)

Author keywords

Clustering validation; Clustering visualization; Co clustering; Gene expression data; Gene function prediction; Gene ontology; Saccharomyces cerevisiae yeast; Self organizing maps

Indexed keywords

DATA STRUCTURES; GENETIC ENGINEERING; ONTOLOGY; SELF ORGANIZING MAPS; YEAST;

CLUSTERING VISUALIZATION; CO-CLUSTERING; GENE EXPRESSION DATA; GENE FUNCTION PREDICTION; GENE ONTOLOGY;

GENE EXPRESSION;

ALGORITHM; ARTICLE; BIOINFORMATICS; CORRELATION ANALYSIS; DATA ANALYSIS; DATA BASE; FUNGAL GENE; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE ONTOLOGY; GENOME; LINGUISTICS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SELF ORGANIZING MAP; VALIDATION PROCESS;

ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; COMPUTER GRAPHICS; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TERMINOLOGY; USER-COMPUTER INTERFACE;

EID: 33847663266     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2006.05.001     Document Type: Article

References (32)

1. Azuaje F. A cluster validity framework for genome expression data. Bioinformatics 18 2 (2002) 319-320
2. Brown M.P., Grundy W.N., Lin D., Cristianini N., Sugnet C.W., Furey T.S., et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 97 1 (2000) 262-267
3. Cheng J., Cline M., Martin J., Finkelstein D., Awad T., Kulp D., et al. A knowledge-based clustering algorithm driven by Gene Ontology. J Biopharm Stat 14 3 (2004) 687-700
4. Cheng J., Sun S., Tracy A., Hubbell E., Morris J., Valmeekam V., et al. NetAffx Gene Ontology mining tool: a visual approach for microarray data analysis. Bioinformatics 20 9 (2004) 1462-1463
5. Cho R.J., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2 1 (1998) 65-73
6. Davies DL. Bouldin, D.W. A cluster separation measure. In: IEEE trans. on pattern analysis and machine intelligence (PAMI); 1979. 1 (4): pp. 224-7.
7. Doniger S.W., Salomonis N., Dahlquist K.D., Vranizan K., Lawlor S.C., and Conklin B.R. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4 (2003) R7
8. Dunn J.C. Well separated clusters and optimal fuzzy partitions. J Cybern 4 (1974) 95-104
9. Dwight S.S., Balakrishnan R., Christie K.R., Costanzo M.C., Dolinski K., Engel S.R., et al. Saccharomyces Genome Database: underlying principles and organisation. Brief Bioinform 5 1 (2004) 9-22
10. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome-wide expression patterns. PNAS Genet 95 (1998) 14863-14868
11. Famili A., Liu G., and Liu Z. Evaluation and optimization of clustering in gene expression data analysis. Bioinformatics 20 10 (2004) 1535-1545
12. Gene Ontology Consortium. (2000) Gene Ontology: tool for the unification of biology. Nat Genet. 25(1):25-9.
13. Gibbons F.D., and Roth F.P. Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res 12 (2002) 1574-1581
14. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 5439 (1999) 531-537
15. Hanisch D., Zien A., Zimmer R., and Lengauer T. Co-clustering of biological networks and gene expression data. Bioinformatics 18 90001 (2002) 145-154
16. Jiang J, Conrath D. Semantic similarity based on corpus statistics and lexical taxonomy. In: Proc. of Int. Conf. on Research in Computational Linguistics (ROCLING), 1997.
17. Kohonen T. Self-organizing maps (1997), Springer, Berlin
18. Lægreid A., Hvidsten T.R., Midelfart H., Komorowski J., and Sandvik A.K. Predicting Gene Ontology biological process from temporal gene expression patterns. Genome Res 13 5 (2003) 965-979
19. Lin D.An information-theoretic definition of similarity. In: Proc. of Int. Conf. on Machine Learning, 1998.
20. Lord P.W., Stevens R., Brass A., and Goble C.A. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19 10 (2003) 1275-1283
21. Quackenbush J. Computational analysis of microarray data. Nat Rev Genet 2 6 (2001) 418-427
22. Resnik P. Using information content to evaluate semantic similarity in a taxonomy. In: Proc. of Int. Joint Conf. on Artificial Intelligence (IJCAI), 1995, pp. 448-53.
23. Speer N, Spieth C, Zell A. A memetic co-clustering algorithm for gene expression profiles and biological annotation. In: Proc. of Congress on Evolutionary Computation (CEC), 2004, vol. 2, pp. 1631-8.
24. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9 12 (1998) 3273-3297
25. Tamayo P., Slonim D., Mesirov J., Zhu Q., Kitareewan S., Dmitrovsky E., et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96 6 (1999) 2907-2912
26. Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene expression correlation and Gene Ontology-based similarity: an assessment of quantitative relationships. In: Proc. of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2004, pp. 25-31.
27. Wu L.F., Hughes T.R., Davierwala A.P., Robinson M.D., Stoughton R., and Altschuler S.J. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet 31 3 (2002) 255-265
28. Yeung K.Y., Haynor D.R., and Ruzzo W.L. Validating clustering for gene expression data. Bioinformatics 17 4 (2001) 309-318
29. Universal Protein Resource (UniProt) .
30. Saccharomyces Genome Database (SGD) .
31. GO Slim annotations .
32. Spellman expression dataset .