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Relational Subgroup Discovery for Descriptive Analysis of Microarray Data

  • Igor Trajkovski
  • Filip Železný
  • Jakub Tolar
  • Nada Lavrač
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4216)

Abstract

This paper presents a method that uses gene ontologies, together with the paradigm of relational subgroup discovery, to help find description of groups of genes differentially expressed in specific cancers. The descriptions are represented by means of relational features, extracted from gene ontology information, and are straightforwardly interpretable by the medical experts. We applied the proposed method to two known data sets: acute lymphoblastic leukemia (ALL) vs. acute myeloid leukemia and classification of fourteen types of cancer. Significant number of discovered groups of genes had a description, confirmed by the medical expert, which highlighted the underlying biological process that is responsible for distinguishing one class from the other classes. We view our methodology not just as a prototypical example of applying sophisticated machine learning algorithms to microarray data, but also as a motivation for developing more sophisticated functional annotations and ontologies, that can be processed by such learning algorithms.

Keywords

Gene Ontology Acute Myeloid Leukemia Acute Lymphoblastic Leukemia Gene Expression Data Inductive Logic Programming 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Igor Trajkovski
    • 1
  • Filip Železný
    • 2
  • Jakub Tolar
    • 3
  • Nada Lavrač
    • 1
  1. 1.Department of Knowledge Technologies, Jozef Stefan InstituteLjubljanaSlovenia
  2. 2.Department of CyberneticsCzech Technical University in PraguePraha 6Czech Republic
  3. 3.Department of PediatricsUniversity of Minnesota Medical SchoolMinneapolisUSA

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