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
Externally publishedYes

Fingerprint

DNA Microarray
Microarrays
Microarray Data
Oligonucleotide Array Sequence Analysis
DNA
Genes
Gene
Interaction
Fine Structure
Leukemia
Iterative Procedure
Gene Expression Data
Random Vector
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Gene expression
Acute
Higher Order
Binary
Gene Expression
Cell

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Gene interaction in DNA microarray data is decomposed by information geometric measure. / Nakahara, Hiroyuki; Nishimura, Shin Ichi; Inoue, Masato; Hori, Gen; Amari, Shun Ichi.

In: Bioinformatics, Vol. 19, No. 9, 12.06.2003, p. 1124-1131.

Research output: Contribution to journalArticle

Nakahara, Hiroyuki ; Nishimura, Shin Ichi ; Inoue, Masato ; Hori, Gen ; Amari, Shun Ichi. / Gene interaction in DNA microarray data is decomposed by information geometric measure. In: Bioinformatics. 2003 ; Vol. 19, No. 9. pp. 1124-1131.
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