title: Automatic annotation of genomic regulatory sequences by searching for composite clusters.
abstract: A new method was developed for revealing of composite clusters of cis-elements in promoters of eukaryotic genes that are functionally related or coexpressed. A software system "ClusterScan" have been created that enables: (i) to train system on representative samples of promoters to reveal cis-elements that tend to cluster, (ii) to train system on a number of samples of functionally related promoters to identify functionally coupled transcription factors; (iii) to provide tools for searching of this clusters in genomic sequences to identify and functionally characterize regulatory regions in genome. A number of training samples of different functional and structural groups of promoters were analysed. Search for composite clusters in human chromosomes 21 and 22 reveals a number of interesting examples. Finally, a decision tree system was constructed to classify promoters of several functionally related gene groups. The decision tree system enables to identify new promoters and computationally predict their possible function.
authors.affiliation: BIOBASE GmbH, Halchtersche Strasse 33, 38304 Wolfenbuettel, Germany.
authors.forename: O V
authors.initials: OV
authors.lastname: Kel-Margoulis
authors.forename: T G
authors.initials: TG
authors.lastname: Ivanova
authors.forename: E
authors.initials: E
authors.lastname: Wingender
authors.forename: A E
authors.initials: AE
authors.lastname: Kel
mesh_terms: D000818:Animals; D001331:Automation; D016000:Cluster Analysis; D016208:Databases, Factual; D003663:Decision Trees; D023281:Genomics; D008322:Mammals / Q000235:genetics; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors