Gene interaction in DNA microarray data is decomposed by information geometric measure

Hiroyuki Nakahara, Shin Ichi Nishimura, Masato Inoue, Gen Hori, Shun Ichi Amari

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Motivation: Given the vast amount of gene expression data, it is essential to develop a simple and reliable method of investigating the fine structure of gene interaction. We show how an information geometric measure achieves this. Results: We introduce an information geometric measure of binary random vectors and show how this measure reveals the fine structure of gene interaction. In particular, we propose an iterative procedure by using this measure (called IPIG). The procedure finds higher-order dependencies which may underlie the interaction between two genes of interest. To demonstrate the method, we investigate the interaction between the two genes of interest in the data from human acute lymphoblastic leukemia cells. The method successfully discovered biologically known findings and also selected other genes as hidden causes that constitute the interaction.

Original languageEnglish
Pages (from-to)1124-1131
Number of pages8
JournalBioinformatics
Volume19
Issue number9
DOIs
Publication statusPublished - 2003 Jun 12

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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