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Evaluation of Semantic Term and Gene Similarity Measures

  • Michal Kozielski
  • Aleksandra Gruca
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6744)

Abstract

In this paper we present the results of the research verifying how the functional description of genes contained in Gene Ontology database is related to genes expression values recorded during biological experiments. We compare several different gene similarity measures and semantic term similarity measures, and evaluate how the similarity of genes based on Gene Ontology terms is correlated with similarity of genes based on expression profiles. The analysis are preformed on three different datasets and we show that there is no single term similarity measure that always gives the best correlation results. The choice of the best term similarity measure depends on dataset characteristic.

Keywords

genes similarity semantic term similarity Gene Ontology database experssion analysis 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Michal Kozielski
    • 1
  • Aleksandra Gruca
    • 1
  1. 1.Silesian University of TechnologyGliwicePoland

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