Minimum cost spanning tree situations and gene expression data analysis

ACM International Conference Proceeding Series

Volumn 199, Issue , 2006, Pages

  Moretti, Stefano ^a  

^a UNIVERSITY OF GENOA   (Italy)

Author keywords

Cooperative game theory; Gene expression analysis; Microarray; Minimum costs spanning tree situation

Indexed keywords

COST REDUCTION; DATA REDUCTION; GAME THEORY; GENE EXPRESSION; MATHEMATICAL MODELS; MICROARRAYS;

COOPERATIVE GAME THEORY; GENE EXPRESSION ANALYSIS; MINIMUM COSTS SPANNING TREE SITUATION;

TREES (MATHEMATICS);

EID: 34748860900     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1190195.1190203     Document Type: Conference Paper

References (32)

1. Allocco D.j., Konane I.S., Butte J. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics, 2004, 5(18).
2. Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., Levine A.J. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissue probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 1999, 96:6745-6750.
3. Amaratunga D., Cabrera J. Exploration and Analysis of DNA Microarray and Protein Array Data, Wiley-Interscience, New Jersey, 2004.
4. Bird C.G. (1976) On cost allocation for a, spanning tree: a game theoretic approach. Networks 6:335-350.
5. Branzei R., Moretti S., Norde H., Tijs S. The P-value for cost sharing in minimum cost spanning tree situations, Theory and Decision, 2004, 56:47-61.
6. Feltkamp V., Tijs S., Muto S. On the irreducible core and the equal remaining obligations rule of minimum cost spanning extension problems, CentER DP 1994 nr.106, Tilburg University, The Netherlands, 1994.
7. Granot D., Huberman G. On minimum cost spanning tree games, Mathematical Programming, 1981, 21:1-18.
8. Heyer L., Kruglyak S., Yooseph S. Exploring Expression Data,: Identification and Analysis of Coexpressed Genes, Genome Research, 1999, 9:1106-1115.
9. de Hoon M., Imoto S., Miyano S. A comparison of clustering techniques for gene expression data. In Proc. of the 10th Intl Conf. on Intelligent Systems for Molecular Biology, 2002.
10. Eliassi-Rad T., Critchlow T. Similarity in Computational Sciences, invited contribution to Abstracts from the 2005 Learning Workshop, Snowbird, UT, April, 2005.
11. Eisen M.B., Spellman P.T., Brown P.O., and Botstein D. Cluster analysis and display of genome wide expression patterns. In PNAS U.S.A., 1998, 95(25):14863-14868.
12. Ewing R.M., Claverie J.M. EST databases as multiconditional gene expression dataseis. Pac. Symp. Biocomput., 2000, 5:427439.
13. Kruskal J.B. On the shortest spanning subtree of a graph and the traveling salesman problem. Proceedings of the American Mathematical Society, 1956, 7:48-50.
14. Genomics:GTL Gene Regulatory Networks, program of the Office of Biological and Environmental Research and Office of Advanced Scientific Computing Research of the U.S. Department of Energy Office of Science, 2005. http://doegenomestolife.org/
15. MacQueen J.B. Some Methods for classification and Analysis of Multivariate Observations, Proceedings of 5-th Berkeley Symposium on Mathematical Statistics and Probability", Berkeley, University of California Press, 1967, 1:281-297.
16. Moretti S. Game Theory applied to gene expression analysis, PhD Dissertation, University of Genoa, Italy, 2006.
17. Moretti S., Patrone F., Bonassi S. The class of Microarray games and the relevance index for genes, presented at the VI Spanish Meeting on Game Theory and Practice, July 12-14, 2004, Elche, Spain (Preprint n.531 of the Department of Mathematics).
18. Norde H. Moretti S., Tijs S. Minimum cost spanning tree games and population monotonie allocation schemes, European Journal of Operational Research, 2004, 154:84-97.
19. Pasanen T., Saarela J., Saarikko I., Toivanen T., Tolvanen M., Vihinen M., Wong. G. In: DNA Microarray Data, Analysis, CSC - Scientific Computing Ltd, Finland, 2003, 161 pages.
20. Prim R.C. Shortest connection networks and some generalizations. Bell Systems Technical Journal, 1957, 36:1389-1401.
21. R. Development Core Team. R: A language and environment for statistical, R, Foundation for Statistical Computing, Vienna, Austria, 2004. http://www.R-project.org
22. Shapley L. S. A Value for n-Person Games, in Contributions to the Theory of Games II (Annals of Mathematics Studies 28), H. W. Kuhn and A. W. Tucker (eds.), Princeton University Press, 1953, 307-317.
23. Shapley L.S., Shubik M. A Method for Evaluating the Distribution of Power in a Committee System, American Political Science R,eview, 1954, 48:787-792.
24. Slonim D., Tamayo P., Mesirov J., Golub T., Lander E. Class Prediction and Discovery Using Gene Expression Data, RECOMB, 2000, 263-272.
25. Speer N., Spieth C., Merz P. Zell A. Clustering Gene Expression Data with Memetic Algorithms based on Minimum Spanning Trees", In Proceedings of the 2003 Congress on Evolutionary Computation, IEEE Press, 2003, 3:1848-1855.
26. Tijs S., Branzei R., Moretti S., Norde H. Obligation rules for minimum cost spanning tree situations and their monotonicity properties, CentER, DP 2004-53, Tilburg University, The Netherlands (European Journal of Operational Research, in press).
27. Tijs S., Moretti S., Branzei R., Norde H. The Bird core for minimum cost spanning tree problems revisited: monotonicity and additivity aspects. Recent Advances in Optimization, Lectures Notes in Economics and Mathematical Systems, Springer-Verlag ed., 2005, 563:305-322.
28. Xu Y, Olman V., Xu D. Minimum spanning trees for gene expression data clustering. Genome Inform Ser Workshop Genome Inform, 2001, 12:24-33.
29. Wagner A. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics, 1999, 15(10):776-84.
30. Wertheimer M. Laws of Organization in Perceptual Forms Max Wertheimer, First published as Untersuchungen zur Lehre von der Gestalt II, in Psycologische Forschung, 1923, 4:301-350. (Translation published in Ellis, W. (1938) A source book of Gestalt psychology, pp. 71-88. London: Routledge Sz Kegan Paul.)
31. Zahn C.T. Graph-theoretical methods for detecting and describing gestalt clusters. IEEE Transactions on Computers, 1971, C-20:6886.
32. Zhu J., Zhang M.Q. Cluster, function and promoter: analysis of yeast expression array. Pac. Symp. Biocomput, 2000, 479-490.