TCLUST: A fast method for clustering genome-scale expression data

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 8, Issue 3, 2011, Pages 808-818

  Dost, Banu ^a   Wu, Chunlei ^b   Su, Andrew ^b   Bafna, Vineet ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

Author keywords

clustering; coconnectedness; graph algorithms; Microarray expression

Indexed keywords

CLUSTERING; CLUSTERING METHODS; COCONNECTEDNESS; DATA SETS; EXPRESSION DATA; EXPRESSION LEVELS; FAST METHODS; GENE EXPRESSION DATA; GRAPH ALGORITHMS; K-MEANS; LARGE DATASETS; MICROARRAY EXPRESSION; MRNA EXPRESSION; NOVEL CLUSTERING; SOURCE CODES;

CLUSTER ANALYSIS; GENE EXPRESSION;

CLUSTERING ALGORITHMS;

ALGORITHM; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; COMPUTER SIMULATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENOMICS; METHODOLOGY; MOUSE; MOUSE STRAIN;

ALGORITHMS; ANIMALS; CLUSTER ANALYSIS; COMPUTER SIMULATION; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENOMICS; MICE; MICE, INBRED STRAINS; MODELS, MOLECULAR; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 79952839584     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2010.34     Document Type: Article

References (24)

1. R. Shamir, R. Sharan, and D. Tsur, "Cluster Graph Modification Problems", Discrete Applied Math., vol. 144, nos. 1/2, pp. 173-182, http://dx.doi.org/10.1016/j.dam.2004.01.007, 2004.
2. S. Delvaux and L. Horsten, "On Best Transitive Approximations to Simple Graphs", Acta Informatica, vol. 40, no. 9, pp. 637-655, 2004. (Pubitemid 39334778)
3. M. R. Garey and D. S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman and Company, 1979.
4. J. Quackenbush, "Computational Analysis of Microarray Data", Nature Rev. Genetics, vol. 2, no. 6, pp. 418-427, http://dx.doi.org/10.1038/ 35076576, June 2001. (Pubitemid 33673408)
5. M. Gerstein and R. Jansen, "The Current Excitement in Bioinformatics-Analysis of Whole Genome Expression Data: How Does It Related to Protein Structure and Function", citeseer.ist.psu. edu/gerstein00current. html, 2000.
6. A. Ben-Dor, R. Shamir, and Z. Yakhini, "Clustering Gene Expression Patterns", J. Computational Biology, vol. 6, nos. 3/4, pp. 281-297, citeseer.ist.psu.edu/ben-dor99clustering.html, 1999.
7. F. D. Gibbons and F. P. Roth, "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation", Genome Research, vol. 12, no. 10, pp. 1574-1581, http://www.hubmed.org/display.cgi? uids=12368250, Oct. 2002. (Pubitemid 35175096)
8. S. Rahmann, T. Wittkop, J. Baumbach, M. Martin, A. Truss, and S. Böcker, "Exact and Heuristic Algorithms for Weighted Cluster Editing", Proc. Computational Systems Bioinformatics Conf, vol. 6, pp. 391-401, http://view.ncbi.nlm.nih.gov/pubmed/17951842, 2007.
9. E. E. Schadt, S. A. Monks, T. A. Drake, A. J. Lusis, N. Che, V. Colinayo, T. G. Ruff, S. B. Milligan, J. R. Lamb, G. Cavet, P. S. Linsley, M. Mao, R. B. Stoughton, and S. H. Friend, "Genetics of Gene Expression Surveyed in Maize, Mouse and Man", Nature, vol. 422, no. 6929, pp. 297-302, http://dx.doi.org/10.1038/nature01434, Mar. 2003. (Pubitemid 36378355)
10. C. Huttenhower, A. I. Flamholz, J. N. Landis, S. Sahi, C. L. Myers, K. L. Olszewski, M. A. Hibbs, N. O. Siemers, O. G. Troyanskaya, and H. A. Coller, "Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods", BMC Bioinformatics, vol. 8, pp. 250-262, 2007.
11. N. Song, J. M. Joseph, G. B. Davis, and D. Durand, "Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins", PLoS Computational Biology, vol. 4, no. 4, http://dx.doi.org/10.1371/journal.pcbi. 1000063, Apr. 2008.
12. R. Motwani and P. Raghavan, Randomized Algorithms. Cambridge Univ. Press, 1995.
13. D. Gibson, R. Kumar, and A. Tomkins, "Discovering Large Dense Subgraphs in Massive Graphs", Proc. 31st Int'l Conf. Very Large Data Bases (VLDB'05), pp. 721-732, 2005. (Pubitemid 43991047)
14. R. Project, The R Project for Statistical Computing, www.r-project.org, 2003.
15. M. Kanehisa, M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, and Y. Yamanishi, "Kegg for Linking Genomes to Life and the Environment", Nucleic Acids Research, gkm882+, vol. 36, pp. D480-484, http://dx.doi.org/10.1093/nar/gkm882, Dec. 2007.
16. Ingenuity Systems "Ingenuity Systems Pathway Analysis", www.ingenuity.com, 2010.
17. M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock, "Gene Ontology: Tool for the Unification of Biology. The Gene Ontology Consortium", Nature Genetics, vol. 25, no. 1, pp. 25-29, http://dx.doi.org/10.1038/75556, May 2000. (Pubitemid 30257031)
18. M. A. Bogue, S. C. Grubb, T. P. Maddatu, and C. J. Bult, "Mouse Phenome Database (mpd)", Nucleic Acids Research, vol. 35, pp. 643-649, http://dblp. uni-trier.de/db/journals/nar/nar35.html#BogueGMB07, 2007.
19. Z. Yingyao, A. Young, S. Andrey, C. Kaisheng, Y. S. Frank, and A. Winzeler, "In Silico Gene Function Prediction Using Ontology-Based Pattern Identification", Bioinformatics, vol. 21, no. 7, pp. 1237-1245, http://dx.doi.org/10.1093/bioinformatics/bti111, Apr. 2005.
20. E. H. A. M. Gordon and M. Regnier, "Regulation of Contraction in Striated Muscle", 2000.
21. C. A. Conley, K. L. Fritz-Six, A. Almenar-Queralt, and V. M. Fowler, "Leiomodins: Larger Members of the Tropomodulin (tmod) Gene Family", Genomics, vol. 73, no. 1, pp. 127-139, http://www.sciencedirect.com/science/ article/B6WG1-45BCMW0-1/2/e5ef9707cbe3d3959295dd41cf114e56, May 2001. (Pubitemid 32411350)
22. K. Brix, P. Lemansky, and V. Herzog, "Evidence for Extracellularly Acting Cathepsins Mediating Thyroid Hormone Liberation in Thyroid Epithelial Cells", Endocrinology, vol. 137, no. 5, pp. 1963-1974, http://www.hubmed. org/display.cgi? uids=8612537, May 1996. (Pubitemid 26139692)
23. L. Gautier, L. Cope, B. M. Bolstad, and R. A. Irizarry, "Affy-Analysis of Affymetrix Genechip Data at the Probe Level", Bioinformatics, vol. 20, no. 3, pp. 307-315, 2004. (Pubitemid 38262761)
24. R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smythy, L. Tierney, J. Y. Yang, and J. Zhang, "Bioconductor: Open Software Development for Computational Biology and Bioinformatics", Genome Biology, vol. 5, no. 10, pp. 80-95, http://dx.doi.org/10.1186/gb-2004-5-10-r80, 2004.