title: Homotypic regulatory clusters in Drosophila.
abstract: Cis-regulatory modules (CRMs) are transcription regulatory DNA segments (approximately 1 Kb range) that control the expression of developmental genes in higher eukaryotes. We analyzed clustering of known binding motifs for transcription factors (TFs) in over 60 known CRMs from 20 Drosophila developmental genes, and we present evidence that each type of recognition motif forms significant clusters within the regulatory regions regulated by the corresponding TF. We demonstrate how a search with a single binding motif can be applied to explore gene regulatory networks and to discover coregulated genes in the genome. We also discuss the potential of the clustering method in interpreting the differential response of genes to various levels of transcriptional regulators.
authors.affiliation: Institute of Chemical Physics, Moscow, 117421 Russia.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Lifanov
authors.forename: Vsevolod J
authors.initials: VJ
authors.lastname: Makeev
authors.forename: Anna G
authors.initials: AG
authors.lastname: Nazina
authors.forename: Dmitri A
authors.initials: DA
authors.lastname: Papatsenko
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D004331:Drosophila melanogaster / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental / Q000235:genetics / Q000502:physiology; D005801:Genes, Homeobox / Q000235:genetics; D017344:Genes, Insect / Q000235:genetics; D005809:Genes, Regulator / Q000235:genetics; D005810:Multigene Family / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology
chemical_list: D014157:Transcription Factors