A new framework for co-clustering of gene expression data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7036 LNBI, Issue , 2011, Pages 1-12

  Zhang, Shuzhong ^a,c   Wang, Kun ^b   Chen, Bilian ^c   Huang, Xiuzhen ^b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b ARKANSAS STATE UNIVERSITY   (United States)

^c CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING QUALITY; CO-CLUSTERING; DEVELOPMENT STAGES; EXPERIMENTAL TESTING; GENE EXPRESSION DATA; GENE EXPRESSION DATASETS; HIGH-DIMENSIONAL; MICROARRAY GENE EXPRESSION; OPTIMIZATION METHOD; OPTIMIZATION MODELS; TIME POINTS;

ALGORITHMS; BIOINFORMATICS; OPTIMIZATION; PATTERN RECOGNITION; TISSUE;

GENE EXPRESSION;

EID: 80455173664     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-24855-9_1     Document Type: Conference Paper

References (13)

1. Aguilar-Ruiz, J.S.: Shifting and scaling patterns from gene expression data. Bioinformatics 21(20), 3840-3845 (2005)
2. 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., Powell, J.I., Yang, L., Marti, G.E., Moore, T., Hudson Jr., J., Lu, L., Lewis, D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C., Weisenburger, D.D., Armitage, J.O., Warnke, R., Levy, R., Wilson, W., Grever, M.R., Byrd, J.C., Botstein, D., Brown, P.O., Staudt, L.M.: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769), 503-511 (2000)
3. Chen, B., He, S., Li, Z., Zhang, S.: Maximum block improvement and polynomial optimization (submitted for publication, 2011)
4. Cheng, Y., Church, G.M.: Biclustering of expression data. In: Proc. Int. Conf. Intell. Syst. Mol. Biol., vol. 8, pp. 93-103 (2000)
5. Cho, H., Dhillon, I.S., Guan, Y., Sra, S.: Minimum sum-squared residue co-clustering of gene expression data. In: Proceedings of The fourth SIAM International Conference on Data Mining, pp. 114-125 (2004)
6. Hartigan, J.A.: Direct clustering of a data matrix. Journal of the American Statistical Association 67(337), 123-129 (1972)
7. Hochreiter, S., Bodenhofer, U., Heusel, M., Mayr, A., Mitterecker, A., Kasim, A., Khamiakova, T., Sanden, S.V., Lin, D., Talloen, W., Bijnens, L., Ghlmann, H.W.H., Shkedy, Z., Clevert, D.: FABIA: factor analysis for bicluster acquisition. Bioinformatics 26(12), 1520-1527 (2010)
8. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D'Angelo, C., Bornberg-Bauer, E., Kudla, J., Harter, K.: The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. The Plant Journal 2, 347-363 (2007)
9. Kolda, T.G., Bader, B.W.: Tensor decompositions and applications. SIAM Review 51(3), 455-500 (2009)
10. Jegelka, S., Sra, S., Banerjee, A.: Approximation algorithms for tensor clustering. In: Gavaldà, R., Lugosi, G., Zeugmann, T., Zilles, S. (eds.) ALT 2009. LNCS, vol. 5809, pp. 368-383. Springer, Heidelberg (2009)
11. Madeira, S.C., Oliveira, A.L.: Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans. Comput. Biology Bioinform. 1(1), 24-45 (2004)
12. Supper, J., Strauch, M., Wanke, D., Harter, K., Zell, A.: EDISA: extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformatics 8, 334-347 (2007)
13. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., Church, G.: Systematic determination of genetic network architecture. Nat. Genet. 22(3), 281-285 (1999)