title: Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis.
abstract: Microarrays traditionally have been used to assay the transcript expression of coding regions of genes. Here, we use Escherichia coli oligonucleotide microarrays to assay transcript expression of both open reading frames (ORFs) and intergenic regions. We then use hidden Markov models to analyse this expression data and estimate transcription boundaries of genes. This approach allows us to identify 5' untranslated regions (5' UTRs) of transcripts as well as genes that are likely to be operon members. The operon elements we identify correspond to documented operons with 99% specificity and 63% sensitivity. Similarly we find that our 5' UTR results accurately coincide with experimentally verified promoter regions for most genes.
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA. tjaden@cs.washington.edu
authors.forename: Brian
authors.initials: B
authors.lastname: Tjaden
authors.forename: David R
authors.initials: DR
authors.lastname: Haynor
authors.forename: Sergey
authors.initials: S
authors.lastname: Stolyar
authors.forename: Carsten
authors.initials: C
authors.lastname: Rosenow
authors.forename: Eugene
authors.initials: E
authors.lastname: Kolker
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods; D004926:Escherichia coli / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009876:Operon / Q000235:genetics*; D011387:Prokaryotic Cells; D012329:RNA, Bacterial / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D012329:RNA, Bacterial; D014157:Transcription Factors