Frequent Itemsets for Genomic Profiling

  • Jeannette M. de Graaf
  • Renée X. de Menezes
  • Judith M. Boer
  • Walter A. Kosters
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3695)

Abstract

Frequent itemset mining is a promising approach to the study of genomic profiling data. Here a dataset consists of real numbers describing the relative level in which a clone occurs in human DNA for given patient samples. One can then mine, for example, for sets of samples that share some common behavior on the clones, i.e., gains or losses. Frequent itemsets show promising biological expressiveness, can be computed efficiently, and are very flexible. Their visualization provides the biologist with useful information for the discovery of patterns. Also it turns out that the use of (larger) frequent itemsets tends to filter out noise.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Cardoso, J., Molenaar, L., de Menezes, R.X., Rosenberg, C., Morreau, H., Möslein, G., Fodde, R., Boer, J.M.: Genomic Profiling by DNA Amplification of Laser Capture Microdissected Tissues and Array CGH. Nucleic Acids Research 32, e146.1–146.13 (2004)Google Scholar
  2. 2.
    Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning. Springer, Heidelberg (2001)MATHGoogle Scholar
  3. 3.
    Kosters, W.A., Pijls, W.: Apriori: A Depth First Implementation. In: FIMI 2003, Workshop on Frequent Itemset Mining Implementations 2003; CEUR Workshop Proceedings (online; Goethals, B., Zaki, M.J. (eds.))Google Scholar
  4. 4.
    Kosters, W.A., van Wezel, M.C.: Competitive Neural Networks for Customer Choice Models. In: Segovia, J., Szczepaniak, P.S., Niedzwiedzinski, M. (eds.) E-Commerce and Intelligent Models, pp. 41–60. Physica Verlag, Springer, Heidelberg (2002)Google Scholar
  5. 5.
    Lengauer, C., Kinzler, K., Vogelstein, B.: Genetic Instabilities in Human Cancers. Nature 396, 643–649 (1998)CrossRefGoogle Scholar
  6. 6.
    Nakao, K., Mehta, K.R., Fridlyand, J., Moore, D.H., Jain, A.N., Lafuente, A., Wiencke, J.W., Terdiman, J.P., Waldman, F.M.: High-resolution Analysis of DNA Copy Number Alterations in Colorectal Cancer by Array-based Comparative Genomic Hybridization. Carcinogenesis 25, 1345–1357 (2004)CrossRefGoogle Scholar
  7. 7.
    Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.L., Chen, C., Zhai, Y., Dairkee, S.H., Ljung, B.M., Gray, J.W., Albertson, D.G.: High Resolution Analysis of DNA Copy Number Variation Using Comparative Genomic Hybridization to Microarrays. Nature Genetics 20, 207–211 (1998)CrossRefGoogle Scholar
  8. 8.
    Rouveirol, C., Radvanyi, F.: Local Pattern Discovery in Array-CGH Data. In: Boulicaut, J.F., Morik, K., Siebes, A. (eds.) Proceedings Dagstuhl Workshop on Detecting Local Patterns. LNCS (LNAI). Springer, Heidelberg (2005) (to appear)Google Scholar
  9. 9.
    Solinas-Toldo, S., Lampel, S., Stilgenbauer, S., Nickolenko, L., Benner, A., Dohner, H., Cremer, T., Lichter, P.: Matrix-based Comparative Genomic Hybridization: Biochips to Screen for Genomic Imbalances. Genes Chromosomes Cancer 20, 399–407 (1997)CrossRefGoogle Scholar
  10. 10.
    Tuzhilin, A., Adomavicius, G.: Handling Very Large Numbers of Association Rules in the Analysis of Microarray Data. In: Proceedings of the Eighth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 396–404. ACM Press, New York (2002)CrossRefGoogle Scholar
  11. 11.
    Zhang, C., Zhang, S.: Association Rule Mining. In: Zhang, C., Zhang, S. (eds.) Association Rule Mining. LNCS (LNAI), vol. 2307, p. 25. Springer, Heidelberg (2002)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Jeannette M. de Graaf
    • 1
  • Renée X. de Menezes
    • 2
    • 3
  • Judith M. Boer
    • 2
  • Walter A. Kosters
    • 1
  1. 1.Leiden Institute of Advanced Computer ScienceUniversiteit LeidenLeidenThe Netherlands
  2. 2.Center for Human and Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
  3. 3.Laboratory of PediatricsErasmus Medical CenterRotterdamThe Netherlands

Personalised recommendations