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

Hiroyuki Nakahara·Shin-ichi Nishimura·Masato Inoue·Gen Hori·Shun-ichi Amari
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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. AVAILABILITY: Softwares are currently not available but are possibly made available in future at http://www.mns.brain.riken.go.jp/~nakahara/DNA_pub.html where all the related information is also linked.

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AlgorithmsCluster AnalysisDNA-Binding ProteinsEpistasis, GeneticFeasibility StudiesGene Expression ProfilingGene Expression RegulationGene Expression Regulation, NeoplasticHumansImmunoglobulin Heavy ChainsModels, GeneticModels, StatisticalOligonucleotide Array Sequence AnalysisPrecursor Cell Lymphoblastic Leukemia-LymphomaRegulatory Factor X Transcription FactorsSequence Analysis, DNASequence Homology, Nucleic AcidStatistics as TopicTranscription FactorsEvaluation StudyJournal ArticleValidation Study

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Hiroyuki Nakahara, Shin-ichi Nishimura, Masato Inoue, Gen Hori, Shun-ichi Amari. 2003-06-12. Gene interaction in DNA microarray data is decomposed by information geometric measure.. https://doi.org/10.1093/bioinformatics%2Fbtg098

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