Finding dominant sets in microarray data

Frontiers in Bioscience

Volumn 10, Issue SUPPL. 3, 2005, Pages 3068-3077

  Fu, Xuping ^a   Teng, Li ^b   Li, Yao ^a   Chen, Wenbin ^b   Mao, Yumin ^a   Shen, I Fan ^b   Xie, Yi ^a  

^a FUDAN UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

Author keywords

Cluster; Correlation coefficient; Dominant sets; Microarray data; Significance level

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; CELL CYCLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENE EXPRESSION; GENETICS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; QUALITATIVE ANALYSIS; STATISTICAL SIGNIFICANCE;

EID: 21344453802     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/1763     Document Type: Article

References (21)

1. Eisen M. B, P. T. Spellman, P. O. Brown & D. Botstein: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95, 14863-14868 (1998)
2. Tamayo P, D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E. S. Lander & T. R. Golub: Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 96, 2907-12 (1999)
3. Tavazoie S, J. D. Hughes, M. J. Campbell, R. J. Cho & G. M. Church: Systematic determination of genetic network architecture. Nat Genet 22, 281-5 (1999)
4. Quackenbush J: Computational analysis of microarray data. Nat Rev Genet 2, 418-27 (2001)
5. Alter O, P. O. Brown & D. Botstein: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97, 10101-10106 (2000)
6. De Smet F, J. Mathys, K. Marchal, G. Thijs, B. De Moor & Y. Moreau: Adaptive quality-based clustering of gene expression profiles. Bioinformatics 18, 735-746 (2002)
7. Zahn C. T: Graph-theoretic methods for detecting and describing restalt clusters. IEEE Trans.Comput 68-86 (1971)
8. Ben-Dor A, R. Shamir & Z. Yakhini: Clustering gene expression patterns. J Comput Biol 6, 281-97 (1999)
9. Xing E. P & R. M. Karp: CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts. Bioinformatics 17 Suppl 1, S315 (2001)
10. Pavan, M & M. Pelillo: A new graph-theoretic approach to clustering and segmentation. In CVPR'03 I 145-152 (2003)
11. Motzkin T.S & E. G. Straus: Maxima for graphs and a new proof of a theorem of Turan. Canad J Math 17, 535-540 (1965)
12. Spellman P.T, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, D. Botstein & B. Futcher: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3297 (1998)
13. Ji X. L, J. Li_ling & Z. R. Sun.: Mining gene expression data using a novel approach based on hidden Markov medels. FEBS Letters 542, 125-131 (2003)
14. Iyer V. R, M. B. Eisen, D. T. Ross, G. Schuler, T. Moore, J. C. Lee, J. M. Trent, L. M. Staudt, J. Hudson Jr, M. S. Boguski, D. Lashkari, D. Shalon, D. Botstein & P. O. Brown: The transcriptional program in the response of human fibroblasts to serum. Science 283, 83-7 (1999)
15. Xu Y, V. Olman, D. Xu: Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics 18, 536-45 (2002)
16. Cho R. J, M. J. Campbell, E. A. Winzeler, L. Steinmetz, A. Conway, L. Wodicka, T. G. Wolfsberg, A. E. Gabrielian, D. Landsman, D. J. Lockhart & R. W. Davis: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2, 65-73 (1998)
17. Robinson M. D, J. Grigull, N. Mohammad & T. R. Hughes: FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics 3, 35 (2002) [The software is available at http://funspec.med.utoronto.ca]
18. Getz G, E. Levine, E. Domany & M. Q. Zhang: Super-paramagnetic clustering of yeast gene expression profiles. Physics A 279, 457-464 (2000)
19. Tavazoie S, J. D. Hughes, M. J. Campbell, R. J. Cho & G. M. Church: Systematic determination of genetic network architecture. Nat Genet 22, 281-5 (1999)
20. Heyer L. J, S. Kruglyak & S. Yooseph: Exploring expression data: identification and analysis of coexpressed genes. Genome Res 9, 1106-1115 (1999)
21. Zhu J & M. Q. Zhang. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15, 607-611 (1999).