title: Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA.
abstract: BACKGROUND
  Sites in DNA that bind regulatory proteins can be detected computationally in various ways. Pattern discovery methods analyze collections of genes suspected to be co-regulated on the evidence, for example, of clustering of transcriptome data. Pattern searching methods use sequences with known binding sites to find other genes regulated by a given protein. Such computational methods are important strategies in the discovery and elaboration of regulatory networks and can provide the experimental biologist with a precise prediction of a binding site or identify a gene as a member of a set of co-regulated genes (a regulon). As more variations on such methods are published, however, thorough evaluation is necessary, as performance may differ depending on the conditions of use. Detailed evaluation also helps to improve and understand the behavior of the different methods and computational strategies.
  
  
  RESULTS
  We used a collection of 86 regulons from Escherichia coli as datasets to evaluate two methods for pattern discovery and pattern searching: dyad analysis/dyad sweeping using the program Dyad-analysis, and multiple alignment using the programs Consensus/Patser. Clearly defined statistical parameters are used to evaluate the two methods in different situations. We placed particular emphasis on minimizing the rate of false positives.
  
  
  CONCLUSIONS
  As a general rule, sensors obtained from experimentally reported binding sites in DNA frequently locate true sites as the highest-scoring sequences within a given upstream region, especially using Consensus/Patser. Pattern discovery is still an unsolved problem, although in the cases where Dyad-analysis finds significant dyads (around 50%), these frequently correspond to true binding sites. With more robust methods, regulatory predictions could help identify the function of unknown genes.
authors.affiliation: Program of Computational Genomics, CIFN, UNAM, A,P, 565-A, Cuernavaca, Morelos 62100, Mexico. moreno@cim.unam.mx
authors.forename: Esperanza
authors.initials: E
authors.lastname: Benítez-Bellón
authors.forename: Gabriel
authors.initials: G
authors.lastname: Moreno-Hagelsieb
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D018085:Regulon / Q000235:genetics; D012097:Repressor Proteins / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012697:Serine Endopeptidases / Q000378:metabolism; D000099160:LexA Repressor Protein
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; D012697:Serine Endopeptidases; D000099160:LexA Repressor Protein