Two FCA-Based Methods for Mining Gene Expression Data

  • Authors:
  • Mehdi Kaytoue;Sébastien Duplessis;Sergei O. Kuznetsov;Amedeo Napoli

  • Affiliations:
  • Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Vandœuvre-lès-Nancy, France;UMR 1136 Institut National de la Recherche Agronomique (INRA) Nancy Université --- Interactions Arbres/Micro-organismes, Champenoux, France 54280;State University Higher School of Economics, Moscow, Russia 125219;Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Vandœuvre-lès-Nancy, France

  • Venue:
  • ICFCA '09 Proceedings of the 7th International Conference on Formal Concept Analysis
  • Year:
  • 2009

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Abstract

Gene expression data are numerical and describe the level of expression of genes in different situations, thus featuring behaviour of the genes. Two methods based on FCA (Formal Concept Analysis) are considered for clustering gene expression data. The first one is based on interordinal scaling and can be realized using standard FCA algorithms. The second method is based on pattern structures and needs adaptations of standard algorithms to computing with interval algebra. The two methods are described in details and discussed. The second method is shown to be more computationally efficient and providing more readable results. Experiments with gene expression data are discussed.