Modular analysis of the transcriptional regulatory network of E. coli

Osbaldo Resendis-Antonio; Julio A. Freyre-González; Ricardo Menchaca-Méndez; Rosa M. Gutiérrez-Ríos; Agustino Martínez-Antonio; Cristhian Ávila-Sánchez; Julio Collado-Vides

doi:10.1016/j.tig.2004.11.010

Modular analysis of the transcriptional regulatory network of E. coli

Osbaldo Resendis-Antonio, Julio A. Freyre-González, Ricardo Menchaca-Méndez, Rosa M. Gutiérrez-Ríos, Agustino Martínez-Antonio, Cristhian Ávila-Sánchez, Julio Collado-Vides

Producción científica: Contribución a una revista › Estudio breve › revisión exhaustiva

78 Citas (Scopus)

Resumen

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.

Idioma original	Inglés
Páginas (desde-hasta)	16-20
Número de páginas	5
Publicación	Trends in Genetics
Volumen	21
N.º	1
DOI	https://doi.org/10.1016/j.tig.2004.11.010
Estado	Publicada - ene. 2005
Publicado de forma externa	Sí

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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.",

author = "Osbaldo Resendis-Antonio and Freyre-Gonz{\'a}lez, {Julio A.} and Ricardo Menchaca-M{\'e}ndez and Guti{\'e}rrez-R{\'i}os, {Rosa M.} and Agustino Mart{\'i}nez-Antonio and Cristhian {\'A}vila-S{\'a}nchez and Julio Collado-Vides",

note = "Funding Information: J.F-G. is supported by Ph.D. fellowship 176341 from CONACyT-Mexico. This work is supported by grant GM 62205-03 from NIH to J.C-V. We thank Ver{\'o}nica Jim{\'e}nez for help extracting the dataset from RegulonDB. We also acknowledge Fabiola S{\'a}nchez for her computing support. We acknowledge the Editor for helping to improve this article. ",

year = "2005",

month = jan,

doi = "10.1016/j.tig.2004.11.010",

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T1 - Modular analysis of the transcriptional regulatory network of E. coli

AU - Resendis-Antonio, Osbaldo

AU - Freyre-González, Julio A.

AU - Menchaca-Méndez, Ricardo

AU - Gutiérrez-Ríos, Rosa M.

AU - Martínez-Antonio, Agustino

AU - Ávila-Sánchez, Cristhian

AU - Collado-Vides, Julio

N1 - Funding Information: J.F-G. is supported by Ph.D. fellowship 176341 from CONACyT-Mexico. This work is supported by grant GM 62205-03 from NIH to J.C-V. We thank Verónica Jiménez for help extracting the dataset from RegulonDB. We also acknowledge Fabiola Sánchez for her computing support. We acknowledge the Editor for helping to improve this article.

PY - 2005/1

Y1 - 2005/1

N2 - 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.

AB - 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.

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U2 - 10.1016/j.tig.2004.11.010

DO - 10.1016/j.tig.2004.11.010

M3 - Estudio breve

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VL - 21

SP - 16

EP - 20

JO - Trends in Genetics

JF - Trends in Genetics

IS - 1

ER -

Modular analysis of the transcriptional regulatory network of E. coli

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