Team:Toronto/Modeling

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<h7><font color=black><p style = "text-align:center; font-size:35px;"><b>REGULATORY SYSTEM MAPPING</b></p><br/>
<h7><font color=black><p style = "text-align:center; font-size:35px;"><b>REGULATORY SYSTEM MAPPING</b></p><br/>
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The system map was created to help the team to select genes relevant to biofilm response regulation as targets for characterizing overexpression strains and  
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<p style = "font-size:17px;">The system map was created to help the team to select genes relevant to biofilm response regulation as targets for characterizing overexpression strains and  
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deletion strains. <br/>
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deletion strains. <br/> <br/>
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Species such as proteins, mRNAs, csRNAs, genes, metabolites, etc. are nodes in the map; interactions between the species are represented by lines between them. Arrows indicate positive influence (the product of an enzyme, a ligand binding to a DNA-bound transcriptional repressor, etc.), while lines ending in a single bar indicates negative influence (an enzyme breaking down a signal molecule, a csRNA interfering with transcription, etc.). <br/>
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Environmental stimuli that are external perturbations to the represented system influence a large chain on interactions, some amplificatory, some repressive; hence one use of this diagram can be to overall track which phenotypes a perturbation may affect. Likewise, such a map can also suggest the effect of a gene deletion on the transmission of an environmental stimuli through the regulatory network. <br/>
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Species such as proteins, mRNAs, csRNAs, genes, metabolites, etc. are nodes in the map; interactions between the species are represented by lines between them. Arrows indicate positive influence (the product of an enzyme, a ligand binding to a DNA-bound transcriptional repressor, etc.), while lines ending in a single bar indicates negative influence (an enzyme breaking down a signal molecule, a csRNA interfering with transcription, etc.). <br/> <br/>
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The current version of the system map was made by referring to ECOCYC entries, extracting the regulatory influence data from the entries for each node, and connecting the influences.<br/>
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NOTE: This map was created solely for picking interesting genes, no annotations that make references to ECOCYC were made.<br/>
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Environmental stimuli that perturb the represented system cause a large sequential chain of interactions, some signal-amplifying, some signal-repressing; hence the map can be used to track down the resulting phenotype. Used in another manner, this map can also suggest the effects of a gene deletion on signal transmission pathways for any given environmental stimulus. <br/> <br/>
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The CellDesigner model can be found here: (Insert link here)<br/>
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A .pdf containing the graphic representation can be found here: (Insert link here)
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The current version of the system map was made by referring to ECOCYC entries, extracting the regulatory influence data from the entries for each node, and connecting the influences.<br/><br/>
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NOTE: This map was created solely for picking interesting genes, no annotations to ECOCYC were tracked.<br/>  
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The CellDesigner model can be <a href="https://2013.igem.org/File:System_Map_(Celldesigner)_(Ecocyc_Only).xml.zip">found here. </a><br/>
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A .pdf containing the graphic representation can be<a href="https://static.igem.org/mediawiki/2013/5/5d/System_Map_%28Ecocyc_Only%29.pdf"> found here. </a>
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Latest revision as of 03:52, 28 September 2013





REGULATORY SYSTEM MAPPING


The system map was created to help the team to select genes relevant to biofilm response regulation as targets for characterizing overexpression strains and deletion strains.

Species such as proteins, mRNAs, csRNAs, genes, metabolites, etc. are nodes in the map; interactions between the species are represented by lines between them. Arrows indicate positive influence (the product of an enzyme, a ligand binding to a DNA-bound transcriptional repressor, etc.), while lines ending in a single bar indicates negative influence (an enzyme breaking down a signal molecule, a csRNA interfering with transcription, etc.).

Environmental stimuli that perturb the represented system cause a large sequential chain of interactions, some signal-amplifying, some signal-repressing; hence the map can be used to track down the resulting phenotype. Used in another manner, this map can also suggest the effects of a gene deletion on signal transmission pathways for any given environmental stimulus.

The current version of the system map was made by referring to ECOCYC entries, extracting the regulatory influence data from the entries for each node, and connecting the influences.

NOTE: This map was created solely for picking interesting genes, no annotations to ECOCYC were tracked.
The CellDesigner model can be found here.
A .pdf containing the graphic representation can be found here.




















































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