Dataset Information

Shen-Orr2002_FeedForward_AND_gate

ABSTRACT: This is the coherent feed forward loop with an AND-gate like control of the response operon described in the article: Network motifs in the transcriptional regulation network of Escherichia coli Shai S. Shen-Orr, Ron Milo, Shmoolik Mangan, Uri Alon, Nat Genet 2002 31:64-68; PMID: 11967538 ; DOI: 10.1038/ng881 ; Abstract: Little is known about the design principles of transcriptional regulation networks that control gene expression in cells. Recent advances in data collection and analysis, however, are generating unprecedented amounts of information about gene regulation networks. To understand these complex wiring diagrams, we sought to break down such networks into basic building blocks. We generalize the notion of motifs, widely used for sequence analysis, to the level of networks. We define 'network motifs' as patterns of interconnections that recur in many different parts of a network at frequencies much higher than those found in randomized networks. We applied new algorithms for systematically detecting network motifs to one of the best-characterized regulation networks, that of direct transcriptional interactions in Escherichia coli. We find that much of the network is composed of repeated appearances of three highly significant motifs. Each network motif has a specific function in determining gene expression, such as generating temporal expression programs and governing the responses to fluctuating external signals. The motif structure also allows an easily interpretable view of the entire known transcriptional network of the organism. This approach may help define the basic computational elements of other biological networks. This model reproduces the timecourse presented in Figure 2a. All species and parameters in the model are dimensionless.

SUBMITTER: Kieran Smallbone

PROVIDER: BIOMD0000000316 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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			Action	DRS
	BIOMD0000000316?filename=BIOMD0000000316-biopax2.owl	Owl
	BIOMD0000000316?filename=BIOMD0000000316-biopax3.owl	Owl
	BIOMD0000000316?filename=BIOMD0000000316-matlab.m	Other
	BIOMD0000000316?filename=BIOMD0000000316.m	Other
	BIOMD0000000316?filename=BIOMD0000000316.ode	Other

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Network motifs in the transcriptional regulation network of Escherichia coli.

Shen-Orr Shai S SS Milo Ron R Mangan Shmoolik S Alon Uri U

Nature genetics 20020422 1

Little is known about the design principles of transcriptional regulation networks that control gene expression in cells. Recent advances in data collection and analysis, however, are generating unprecedented amounts of information about gene regulation networks. To understand these complex wiring diagrams, we sought to break down such networks into basic building blocks. We generalize the notion of motifs, widely used for sequence analysis, to the level of networks. We define 'network motifs' a ...[more]

PMID: 11967538

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