title: Modular analysis of the transcriptional regulatory network of E. coli.
abstract: The transcriptional network of Escherichia coli is currently the best-understood regulatory network of a single cell. Motivated by statistical evidence, suggesting a hierarchical modular architecture in this network, we identified eight modules with well-defined physiological functions. These modules were identified by a clustering approach, using the shortest path to trace regulatory relationships across genes in the network. We report the type (feed forward and bifan) and distribution of motifs between and within modules. Feed-forward motifs tend to be embedded within modules, whereas bi-fan motifs tend to link modules, supporting the notion of a hierarchical network with defined functional modules.
authors.affiliation: Program of Computational Genomics, Nitrogen Fixation Research Center, Universidad Nacional Autónoma de México, Ave Universidad s/n, Col Chamilpa, Cuernavaca, Morelos 62100 México.
authors.forename: Osbaldo
authors.initials: O
authors.lastname: Resendis-Antonio
authors.forename: Julio A
authors.initials: JA
authors.lastname: Freyre-González
authors.forename: Ricardo
authors.initials: R
authors.lastname: Menchaca-Méndez
authors.forename: Rosa M
authors.initials: RM
authors.lastname: Gutiérrez-Ríos
authors.forename: Agustino
authors.initials: A
authors.lastname: Martínez-Antonio
authors.forename: Cristhian
authors.initials: C
authors.lastname: Avila-Sánchez
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D008957:Models, Genetic; D010802:Phylogeny; D014158:Transcription, Genetic