title: Predicting rules on organization of cis-regulatory elements, taking the order of elements into account.
abstract: BACKGROUND
  In eukaryotes, rules regarding organization of cis-regulatory elements are complex. They sometimes govern multiple kinds of elements and positional restrictions on elements.
  
  
  RESULTS
  We propose a method for detecting rules, by which the order of elements is restricted. The order restriction is expressed as element patterns. We extract all the element patterns that occur in promoter regions of at least the specified number of genes. Then, we find significant patterns based on the expression similarity of genes with promoter regions containing each of the extracted patterns. When we applied our method to Saccharomyces cerevisiae, we detected significant patterns overlooked by previous methods, thus demonstrating the utility of our method for analyses of eukaryotic gene regulation. We also suggest that several types of element organization exist: (i) those in which only the order of elements is important, (ii) order and distance both are important and (iii) only the combination of elements is important.
  
  
  BACKGROUND
  The program for extracting element patterns is available upon request.
authors.affiliation: INTEC Web and Genome Informatics Corp., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-8637, Japan.
authors.forename: Goro
authors.initials: G
authors.lastname: Terai
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Takagi
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D005809:Genes, Regulator / Q000235:genetics*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*