BioModels Database logo

BioModels Database

spacer

BIOMD0000000317 - Shen-Orr2002_Single_Input_Module

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 11967538
Shen-Orr SS, Milo R, Mangan S, Alon U.
Network motifs in the transcriptional regulation network of Escherichia coli.
Nat. Genet. 2002 May; 31(1): 64-68
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.  [more]
Model
Original Model: BIOMD0000000317.xml.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1102140001
Submission Date: 14 Feb 2011 14:42:09 UTC
Last Modification Date: 31 Mar 2014 12:16:29 UTC
Creation Date: 08 Feb 2011 00:00:00 UTC
Encoders:  Kieran Smallbone
set #1
bqbiol:hasVersion Gene Ontology transcription activator activity
Gene Ontology positive regulation of gene expression
set #2
bqbiol:hasTaxon Taxonomy Escherichia coli
set #3
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #4
bqbiol:isVersionOf Gene Ontology regulation of gene expression
Notes

This is the single input module, SIM, 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 SIM timecourse presented in Figure 2b. All species and parameters in the model are dimensionless.

Model
Publication ID: 11967538 Submission Date: 14 Feb 2011 14:42:09 UTC Last Modification Date: 31 Mar 2014 12:16:29 UTC Creation Date: 08 Feb 2011 00:00:00 UTC
Mathematical expressions
Reactions
r1 r2 r3 r4
r5 r6    
Rules
Rate Rule (variable: X)      
Events
e1 e2    
Physical entities
Compartments Species
cell X Z1 Z2
Z3    
Global parameters
FX      
Reactions (6)
 
 r1  ↔ [Z1];   {X}
 
 r2 [Z1] ↔ ;  
 
 r3  ↔ [Z2];   {X}
 
 r4 [Z2] ↔ ;  
 
 r5  ↔ [Z3];   {X}
 
 r6 [Z3] ↔ ;  
 
Rules (1)
 
 Rate Rule (name: X) d [ X] / d t= FX-X
 
Events (2)
 
 e1
FX = 1
 
 e2
FX = 0
 
Functions (1)
 
 F lambda(X, T, piecewise(1, X >= T, 0))
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 X
Compartment: cell
Initial concentration: 0.0
 
 Z1
Compartment: cell
Initial concentration: 0.0
 
 Z2
Compartment: cell
Initial concentration: 0.0
 
 Z3
Compartment: cell
Initial concentration: 0.0
 
Global Parameters (1)
 
   FX  
 
r1 (1)
 
   T1
Value: 0.1   (Units: dimensionless)
Constant
 
r2 (1)
 
   a
Value: 1.0   (Units: dimensionless)
Constant
 
r3 (1)
 
   T2
Value: 0.5   (Units: dimensionless)
Constant
 
r4 (1)
 
   a
Value: 1.0   (Units: dimensionless)
Constant
 
r5 (1)
 
   T3
Value: 0.8   (Units: dimensionless)
Constant
 
r6 (1)
 
   a
Value: 1.0   (Units: dimensionless)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000317

Curator's comment: (updated: 20 Feb 2011 23:11:06 GMT)

Time courses as in fig 2B of the original publication. Simulations were performed using Copasi 4.6.33.

spacer
spacer