title: Qualitative reasoning of dynamic gene regulatory interactions from gene expression data.
abstract: BACKGROUND
  A gene regulatory relation often changes over time rather than being constant. But many gene regulatory networks available in databases or literatures are static in the sense that they are either snapshots of gene regulatory relations at a time point or union of successive gene regulations over time. Such static networks cannot represent temporal aspects of gene regulatory interactions such as the order of gene regulations or the pace of gene regulations.
  
  
  RESULTS
  We developed a new qualitative method for representing dynamic gene regulatory relations and algorithms for identifying dynamic gene regulations from the time-series gene expression data using two types of scores. The identified gene regulatory interactions and their temporal properties are visualized as a gene regulatory network. All the algorithms have been implemented in a program called GeneNetFinder (http://wilab.inha.ac.kr/genenetfinder/) and tested on several gene expression data.
  
  
  CONCLUSIONS
  The dynamic nature of dynamic gene regulatory interactions can be inferred and represented qualitatively without deriving a set of differential equations describing the interactions. The approach and the program developed in our study would be useful for identifying dynamic gene regulatory interactions from the large amount of gene expression data available and for analyzing the interactions.
authors.affiliation: School of Computer Science and Engineering, Inha University, Incheon, Korea. chenyu@inhaian.net
authors.forename: Yu
authors.initials: Y
authors.lastname: Chen
authors.forename: Byungkyu
authors.initials: B
authors.lastname: Park
authors.forename: Kyungsook
authors.initials: K
authors.lastname: Han
mesh_terms: D000465:Algorithms; D002453:Cell Cycle / Q000235:genetics; D015870:Gene Expression; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005809:Genes, Regulator; D006801:Humans; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013997:Time Factors