Random walk biclustering for microarray data

Information Sciences

Volumn 178, Issue 6, 2008, Pages 1479-1497

  Angiulli, Fabrizio ^a   Cesario, Eugenio ^a   Pizzuti, Clara ^a  

^a ICAR CNR   (Italy)

Author keywords

Biclustering; Local search; Microarray data

Indexed keywords

ALGORITHMS; MATHEMATICAL TRANSFORMATIONS; NUMERICAL METHODS;

BICLUSTERING; EXPERIMENTAL RESULTS; LOCAL SEARCH; RANDOM WALK BICLUSTERING;

MICROARRAYS;

EID: 38349075214     PISSN: 00200255     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ins.2007.11.007     Document Type: Article

References (36)

1. C.C. Aggarwal, C.M. Procopiucand, J.L. Wolf, P.S. Yu, J.S. ParkG, Fast algorithms for projected clustering, in: Proceedings of the ACM International Conference on Management of Data (SIGMOD'99), 1999, pp. 61-72.
2. C.C. Aggarwal, P.S. Yu, Finding generalized projected clusters in high dimensional spaces, in: Proceedings of the ACM International Conference on Management of Data (SIGMOD'00), 2000, pp. 70-81.
3. R. Agrawal, J.C. Gehrke, D. Gunopulos, P. Raghavan, Automatic subspace clustering of high dimensional data for data mining applications, in: Proceedings of the ACM International Conference on Management of Data (SIGMOD'98), 1998, pp. 94-105.
4. Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., and Levine A.J. Broad patterns of gene expression revealed by clustering of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences, USA 96 12 (1999) 6745-6750
5. Azuaje F. A cluster validity framework for genome expression data. Bioinformatics 18 2 (2002) 319-320
6. Azuaje F., and Bolshakova N. Clustering genomic expression data: design and evaluation principles. In: Berrar D.P., Dubitzky W., and Granzow M. (Eds). A Practical Approach to Microarray Data Analysis (2003), Kluwer 230-245
7. Ben Dor A., Shamir R., and Yakhini Z. Clustering gene expression patterns. Journal of Computational Biology 6 3-4 (1999) 281-297
8. S. Busygin, G. Jacobsen, E. Kramer, Double conjugated clustering applied to leukemia microarray data, in: SIAM Data Mining Workshop on Clustering High Dimensional Data and its Applications, 2002.
9. S. Busygin, O. Prokopyev, P.M. Pardalos, Biclustering in data mining, Computers and Operations Research, in press.
10. Busygin S., Prokopyev O., and Pardalos P.M. Feature selection for consistent biclustering via fractional 0-1 programming. Journal of Combinatorial Optimization 10 1 (2005) 7-21
11. Y. Cheng, G.M. Church, Biclustering of expression data, in: Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB'00), 2000, pp. 93-103.
12. H. Cho, I.S. Dhillon, Y. Guan, S. Sra, Minimum sum-squared residue co-clustering of gene expression data, in: Proceedings of the Fourth SIAM International Conference on Data Mining (SDM'04), 2004.
13. I.S. Dhillon, Co-clustering documents and words using bipartite spectral graph partitioning, in: Proceedings of the Seventh International ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD'01), 2003, pp. 269-274.
14. I.S. Dhillon, S. Mallela, D. Modha, Information-theoretic co-clustering, in: Proceedings of the Ninth International ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD'03), 2003, pp. 89-98.
15. Eisen M.B., Spellman P., Brown P.O., and Botstein P. Cluster analysis and display of genome-wide expression pattern. Proceedings of the National Academy of Sciences, USA 8 (1998) 14863-14868
16. Garey M.R., and Johnson D.S. Computers and Intractability: A Guide to the Theory of NP-Completeness (1979), Freeman, San Francisco
17. G. Getz, E. Levine, E. Domany, Coupled two-way cluster analysis of gene microarray data, in: Proceedings of the National Academy of Sciences, USA, 2000, pp. 12079-12084.
18. Grothaus G., Mufti A., and Murali T.M. Automatic layout and visualisation of biclusters. Algorithms for Molecular Biology 21 15 (2006)
19. Halkidi M., Batistakis Y., and Vazirgiannis M. Cluster validity methods: Part I. SIGMOD Record 31 2 (2002) 40-45
20. Halkidi M., Batistakis Y., and Vazirgiannis M. Cluster validity methods: Part II. SIGMOD Record 31 3 (2002) 19-27
21. Hartigan J.A. Direct clustering of a data matrix. Journal of the American Statistical Association 67 337 (1972) 123-129
22. King J.Y., and Ferrara R. Pathway analysis of coronary atherosclerosis. Physiological Genomics 23 1 (2005) 103-118
23. Kluger Y., Basri R., Chang J.T., and Gerstein M. Spectral biclustering of microarray data: coclustering genes and conditions. Genome Research 13 4 (2003) 703-716
24. Lazzeroni L., and Owen A. Plaid models for gene expression data. Statistica Sinica 12 1 (2002) 61-86
25. Madeira S.C., and Oliveira A.L. Biclustering algorithms for biological data analysis: a survey. IEEE Transactions on Computational Biology and Bioinformatics 1 1 (2004) 24-45
26. H. Nagesh, S. Goil, A. Choundhary, Mafia: efficient and scalable subspace clustering for very large datasets, Technical report 9906-010, Northwestern University, 1999.
27. Reiss D.J., Baliga N.S., and Bonneau R. Integrated biclustering of heterogeneous genomewide datasets for the inference of global regulatory networks. BMC Bioinformatics 7 280 (2006)
28. B. Selman, H.A. Kautz, B. Cohen, Noise strategies for improving local search, in: Proceedings of the 12th Nation Conference on Artificial Intelligence (AAAI'94), 1994, pp. 337-343.
29. A. Tanay, Computational Analysis of Transcriptional Programs: Function and Evolution, Ph.D. Thesis, August 2005.
30. Tanay A., Sharan R., Kupiec M., and Shamir R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proceedings of the National Academy of Science 101 (2004) 2981-2986
31. Tanay A., Sharan R., and Shamir R. Discovering statistically significant biclusters in gene expression data. Bioinformatics 18 Suppl. 1 (2002) S136-S144
32. A. Tanay, R. Sharan, R. Shamir, Biclustering algorithms: a survey, in: Srinivas Aluru (Ed.), Handbook of Computation Molecular Biology, 2006.
33. Tavazoie S., Hughes J.D., Campbell M., Cho R.J., and Church G.M. Systematic determination of genetic network architecture. Natural Genetics 22 (1999) 281-285
34. J. Yang, W. Wang, H. Wang, P. Yu, δ-clusters: capturing subspace correlation in a large data set, in: Proceedings of the 18th IEEE International Conference on Data Engineering, 2002, pp. 517-528.
35. J. Yang, W. Wang, H. Wang, P. Yu, Enhanced biclustering on expression data, in: Proceedings of the 3rd IEEE Conference on Bioinformatics and Bioengineering (BIBE'03), 2003, pp. 321-327.
36. Yeung K.Y., Haynor D.R., and Ruzzo W.L. Validating clustering for gene expression data. Bioinformatics 17 4 (2001) 309-318