Noise-robust soft clustering of gene expression time-course data

Journal of Bioinformatics and Computational Biology

Volumn 3, Issue 4, 2005, Pages 965-988

  Futschik, Matthias E ^a,b   Carlisle, Bronwyn ^b  

^a HUMBOLDT UNIVERSITY   (Germany)

^b UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Clustering; Microarray data analysis; Noise robustness

Indexed keywords

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION SYSTEM; NOISE; NONHUMAN; STATISTICAL PARAMETERS; TIME;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; PROTEOME; SOFTWARE; STOCHASTIC PROCESSES; TIME FACTORS;

EID: 22544432531     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720005001375     Document Type: Article

References (20)

1. Jain A, Dubes R, Algorithms for Clustering Data, Prentice Hall, New Jersey, 1988.
2. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM, Systematic determination of genetic network architecture, Nat Genet, 22:281-285, 1999.
3. Törönen P, Kolehmainen M, Wong G, Castren E, Analysis of gene expression data using self-organizing maps, FEBS Lett, 451(2):142-146, 1999.
4. Sharon R, Shamir R, CLICK: A clustering algorithm with applications to gene expression data, Proceedings of the RECOMB 1999, pp. 307-316, 1999.
5. Eisen MB, Spellman PT, Brown PO, Botstein D, Cluster analysis and display of genome-wide expression patterns, Proc Natl Acad Sci USA, 95(1):14863-14868, 1998.
6. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B, Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridisation, Mol Biol Cell, 9(12):3273-3297, 1998.
7. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW, A genome-wide transcriptional analysis of the mitotic cell cycle, Mol Cell, 2:65-73, 1998.
8. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I, The transcriptional program of sporulation in budding yeast, Science, 282(5389):699-705, 1998.
9. Bezdak JC, Pattern Recognition with Fuzzy Objective Function Algorithms, Plenum Press, New York, 1981.
10. Geth I, Geva AB, Unsupervised optimal fuzzy clustering, Trans. Pattern Analysis Machine Intell, 11:773-781, 1989.
11. Duda RO, Hart PE, Stork DG, Pattern Classification, Wiley, New York, 2001.
12. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR, Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation, Proc Natl Acad Sci USA, 96(6):2907-2912, 1999.
13. Lukashin A, Fuchs R, Analysis of temporal gene expression profiles, Bioinformatics, 17(5):405-414, 2000.
14. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB, Missing value estimation methods for DNA microarrays, Bioinformatics 17(6):520-525, 2001.
15. Heyer LJ, Kruglyak S, Yooseph S, Exploring expression data: identification and analysis of coexpressed genes, Genome Res, 11:1106-1115, 1999.
16. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH, Functional discovery via a compendium of expression profiles, Cell, 102(1):109-126, 2000.
17. Roth FP, Hughes JD, Estep PW, Church GM, Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation, Nature Biotech, 16:939-945, 1998.
18. Hughes JD, Estep PW, Tavazoie S, Church GM, Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae, J Mol Biol, 296:1205-1214, 2000.
19. Gasch AP, Eisen MB, Exploring the conditional coregulation of yeast expression through fuzzy k-means clustering, Genome Biology 3(11):research0059.1-0059.22, 2002.
20. Dembele D, Kastner P, Fuzzy c-means method for clustering microarray data, Bioinformatics, 19(8):973-980, 2002.