title: Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.
abstract: BACKGROUND
  Estimating the network of regulative interactions between genes from gene expression measurements is a major challenge. Recently, we have shown that for gene networks of up to around 35 genes, optimal network models can be computed. However, even optimal gene network models will in general contain false edges, since the expression data will not unambiguously point to a single network.
  
  
  RESULTS
  In order to overcome this problem, we present a computational method to enumerate the most likely m networks and to extract a widely common subgraph (denoted as gene network motif) from these. We apply the method to bacterial gene expression data and extensively compare estimation results to knowledge. Our results reveal that gene network motifs are in significantly better agreement to biological knowledge than optimal network models. We also confirm this observation in a series of estimations using synthetic microarray data and compare estimations by our method with previous estimations for yeast. Furthermore, we use our method to estimate similarities and differences of the gene networks that regulate tryptophan metabolism in two related species and thereby demonstrate the analysis of gene network evolution.
  
  
  BACKGROUND
  Commercial license negotiable with Gene Networks Inc. (cherkis@gene-networks.com)
  
  
  BACKGROUND
  sascha-ott@gmx.net
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. sascha-ott@gmx.net
authors.forename: S
authors.initials: S
authors.lastname: Ott
authors.forename: A
authors.initials: A
authors.lastname: Hansen
authors.forename: S-Y
authors.initials: SY
authors.lastname: Kim
authors.forename: S
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000502:physiology; D001426:Bacterial Proteins / Q000378:metabolism; D003198:Computer Simulation; D004926:Escherichia coli / Q000502:physiology; D029968:Escherichia coli Proteins / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D014157:Transcription Factors