CLIC: Clustering analysis of large microarray datasets with individual dimension-based clustering

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Yun, Taegyun ^a   Hwang, Taeho ^a   Cha, Kihoon ^a   Yi, Gwan Su ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION SERVICE PROVIDER; ARTICLE; AUTOANALYSIS; CLUSTER ANALYSIS; CONTENT ANALYSIS; FUNCTIONAL GENOMICS; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC DATABASE; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; PRIORITY JOURNAL; WEB BROWSER; ALGORITHM; COMPUTER PROGRAM; DNA MICROARRAY; HUMAN; INTERNET; TUMOR CELL LINE;

ALGORITHMS; CELL LINE, TUMOR; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; HUMANS; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 77954247705     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq516     Document Type: Article

References (28)

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 arrays. Proc. Natl Acad. Sci. USA, 96, 6745-6750.
3. Golub,T.R., Slonim,D.K., Tamayo,P., Huard,C., Gaasenbeek,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.
4. Perou,C.M., Jeffrey,S.S., van de Rijn,M., Rees,C.A., Eisen,M.B., Ross,D.T., Pergamenschikov,A., Williams,C.F., Zhu,S.X., Lee,J.C. et al. (1999) Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl Acad. Sci. USA, 96, 9212-9217.
5. Pollack,J.R., Perou,C.M., Alizadeh,A.A., Eisen,M.B., Pergamenschikov,A., Williams,C.F., Jeffrey,S.S., Botstein,D. and Brown,P.O. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genetics, 23, 41-46.
6. 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.
7. Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
8. Spellman,P.T., Sherlock,G., Zhang,M.Q., Iyer,V.R., Anders,K., Eisen,M.B., Brown,P.O., Botstein,D. and Futcher,B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
9. Cho,R.J., Campbell,M.J., Winzeler,E.A., Steinmetz,L., Conway,A., Wodicka,L., Wolfsberg,T.G., Gabrielian,A.E., Landsman,D., Lockhart,D.J. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
10. Sharma,A., Podolsky,R., Zhao,J. and McIndoe,R.A. (2009) A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets. Bioinformatics, 25, 1152-1157.
11. Medvedovic,M. and Sivaganesan,S. (2002) Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics, 18, 1194-1206.
12. Qin,Z.S. (2006) Clustering microarray gene expression data using weighted Chinese restaurant process. Bioinformatics, 22, 1988-1997.
13. 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.
14. Har-Peled,S. and Sadri,B. (2005) How fast is the k-means method? Algorithmica, 3, 185-202.
15. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25, 25-29.
16. Kanehisa,M., Araki,M., Goto,S., Hattori,M., Hirakawa,M., Itoh,M., Katayama,T., Kawashima,S., Okuda,S., Tokimatsu,T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
17. Benjamini,Y., Drai,D., Elmer,G., Kafkafi,N. and Golani,I. (2001) Controlling the false discovery rate in behavior genetics research. Behavioural Brain Res., 125, 279-284.
18. Sun,C.H., Kim,M.S., Han,Y. and Yi,G.S. (2009) COFECO: composite function annotation enriched by protein complex data. Nucleic Acids Res., 37, W350-W355.
19. Yeung,K.Y., Fraley,C., Murua,A., Raftery,A.E. and Ruzzo,W.L. (2001) Model-based clustering and data transformations for gene expression data. Bioinformatics, 17, 977-987.
20. Sharan,R. and Shamir,R. (2000) CLICK: a clustering algorithm with applications to gene expression analysis. Proceedings of the 11th. International Conference on Intelligent Systems for Molecular Biology; ISMB. International Conference on Intelligent Systems for Molecular Biology, 8, 307-316.
21. Sharan,R., Maron-Katz,A. and Shamir,R. (2003) CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics, 19, 1787-1799.
22. Geraci,F., Leoncini,M., Montangero,M., Pellegrini,M. and Renda,M.E. (2009) K-Boost: a scalable algorithm for high-quality clustering of microarray gene expression data. J. Comput. Biol., 16, 859-873.
23. Geraci,F., Pellegrini,M. and Renda,M.E. (2008) AMIC@: all microarray clusterings @ once. Nucleic Acids Res., 36, W315-W319.
24. Michaud,D.J., Marsh,A.G. and Dhurjati,P.S. (2003) eXPatGen: generating dynamic expression patterns for the systematic evaluation of analytical methods. Bioinformatics, 19, 1140-1146.
25. Ideker,T., Thorsson,V., Ranish,J.A., Christmas,R., Buhler,J., Eng,J.K., Bumgarner,R., Goodlett,D.R., Aebersold,R. and Hood,L. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292, 929-934.
26. Sun,L., Hui,A.M., Su,Q., Vortmeyer,A., Kotliarov,Y., Pastorino,S., Passaniti,A., Menon,J., Walling,J., Bailey,R. et al. (2006) Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer Cell, 9, 287-300.
27. Ross,D.T., Scherf,U., Eisen,M.B., Perou,C.M., Rees,C., Spellman,P., Iyer,V., Jeffrey,S.S., Van de Rijn,M., Waltham,M. et al. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics, 24, 227-235.
28. Wu,C., Orozco,C., Boyer,J., Leglise,M., Goodale,J., Batalov,S., Hodge,C.L., Haase,J., Janes,J., Huss,J.W. 3rd, et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol., 10, R130.