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


BACKGROUND
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.
Nakahara
Hiroyuki
H
Lab. for Mathematical Neuroscience, RIKEN Brain Science Institute, Saitama 351-0198, Japan. hiro@brain.riken.go.jp
Nishimura
Shin-ichi
S
Inoue
Masato
M
Hori
Gen
G
Amari
Shun-ichi
S
D000465:Algorithms; D016000:Cluster Analysis; D004268:DNA-Binding Proteins / Q000235:genetics; D004843:Epistasis, Genetic; D005240:Feasibility Studies; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*; D000071701:Regulatory Factor X Transcription Factors; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013223:Statistics as Topic; D014157:Transcription Factors / Q000235:genetics
D004268:DNA-Binding Proteins; D007143:Immunoglobulin Heavy Chains; D000071701:Regulatory Factor X Transcription Factors; D014157:Transcription Factors