Context-dependent clustering for dynamic cellular state modeling of microarray gene expression

Bioinformatics

Volumn 23, Issue 22, 2007, Pages 3039-3047

  Yuan, Shinsheng ^a   Li, Ker Chau ^a,b  

^a INSTITUTE OF STATISTICAL SCIENCE   (Taiwan)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CYCLOOXYGENASE 1; CYCLOOXYGENASE 2; CYCLOOXYGENASE 3; SULFUR AMINO ACID; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MET4; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LOCATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC REGULATION; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SCREENING; MATHEMATICAL ANALYSIS; MITOSIS; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 36448943921     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm457     Document Type: Article

References (31)

1. Alon,U. et al. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 96, 6745-6750.
2. Alter,O. et al. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA, 97, 10101-10106.
3. Brown,M.P. et al. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA, 97, 262-267.
4. Chow,M.L. et al. (2001) Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol. Genomics, 5, 99-111.
5. Dempster,A. et al. (1977) Maximum-likehhood from incomplete data via the em algorithm. J. R. Stat. Soc B, 39, 1-38.
6. Doolin,M.-T. et al. (2001) Overlapping and distinct roles of duplicated yeast transcription factors ace2p and swi5p. Mol. Microbiol., 40, 422-432.
7. Eisen,M. B. et al. (1998) Cluster analysis ano display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95 14863-14868.
8. Golub,T.R. et al. (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 15, 531-537.
9. Gordon,D.B. et al. (2005) Tamo: A flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. Bioinformatics, 21, 3164-3165.
10. Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
11. Hughes,T. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
12. Lee,T. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
13. Li,K.-C. (2002) Genome-wide coexpression dynamics: Theory and application. Proc. Natl Acad. Sci. USA, 99, 16875-16880.
14. Li,K.-C. and Yuan,S. (2004) A functional genomic study on nci's anticancer drug screen. Pharmacogenomics J., 4, 127-135.
15. Li,K.-C. et al. (2004) A system for enhancing genome-wide coexpression dynamics study. Proc. Natl Acad. Sci. USA, 101, 15561-15566.
16. Liao,J.C. et al. (2003) Network component analysis: Reconstruction of regulatory signals in biological systems. Proc. Natl Acad. Sci. USA, 100, 15522-15527.
17. Liu,X. et al. (2007) Including probe-level uncertainty in model-based gene expression clustering. BMC Bioinformatics, 8 98.
18. Marcotte,E.M. et al. (1999) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
19. Medvedovic,M. and Sivaganesan,S. (2002) Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics, 18, 1194-1206.
20. Ross,D.T. et al. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet., 24, 227-235.
21. Scherf,U. et al. (2000) A gene expression database for the molecular pharmacology of cancer. Nat. Genet., 24, 236-244.
22. Shi,Y. et al. (2007) Inferring pairwise regulatory relationships from multiple time series datasets. Bioinformatics, 23, 755-763.
23. Spellman,P.T. et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
24. Tamayo,P. et al. (1299) Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.
25. Tseng,G.C. and Wong,W.H. (2005) Tight clustering: A resampling-based approach for identifying stable and tight patterns in data. Biometrics, 61, 10-16.
26. Weaver,R.F. (2002) Molecular Biology. 2nd ed. McGraw-Hill, Boston.
27. Yarragudi,A. et al. (2007) Genome-wide analysis of transcriptional dependence and probable target sites for abf1 and rap1 in Saccharomyces cerevisiae. Nucleic Acids Res., 35, 193-202.
28. Yeung,K.Y. et al. (2001) Model-based clustering and data transformations for gene expression data. Bioinformatics, 17 977-987.
29. Yu,T. and Li,K.-C. (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics, 21, 4033-4038.
30. Zhou,X. et al. (2002) Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl Acad. Sci. USA, 99, 12783-12788.
31. Zhou,X.J. et al. (2005) Functional annotation and network reconstruction through cross-platform integration of microarray data. Nat. Biotechnol., 23, 238-243.