title: GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes.
abstract: BACKGROUND
  The establishment of quantitative gene regulatory networks (qGRNs) through existing network component analysis (NCA) approaches suffers from shortcomings such as usage limitations of problem constraints and the instability of inferred qGRNs. The proposed GeNOSA framework uses a global optimization algorithm (OptNCA) to cope with the stringent limitations of NCA approaches in large-scale qGRNs.
  
  
  RESULTS
  OptNCA performs well against existing NCA-derived algorithms in terms of utilization of connectivity information and reconstruction accuracy of inferred GRNs using synthetic and real Escherichia coli datasets. For comparisons with other non-NCA-derived algorithms, OptNCA without using known qualitative regulations is also evaluated in terms of qualitative assessments using a synthetic Saccharomyces cerevisiae dataset of the DREAM3 challenges. We successfully demonstrate GeNOSA in several applications including deducing condition-dependent regulations, establishing high-consensus qGRNs and validating a sub-network experimentally for dose-response and time-course microarray data, and discovering and experimentally confirming a novel regulation of CRP on AscG.
  
  
  METHODS
  All datasets and the GeNOSA framework are freely available from http://e045.life.nctu.edu.tw/GeNOSA.
  
  
  BACKGROUND
  syho@mail.nctu.edu.tw
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China.
authors.forename: Yi-Hsiung
authors.initials: YH
authors.lastname: Chen
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China.
authors.forename: Chi-Dung
authors.initials: CD
authors.lastname: Yang
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China.
authors.forename: Ching-Ping
authors.initials: CP
authors.lastname: Tseng
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Republic of China.
authors.forename: Shinn-Ying
authors.initials: SY
authors.lastname: Ho
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000235:genetics*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D012441:Saccharomyces cerevisiae / Q000235:genetics*