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Team:Toronto/Modeling
From 2013.igem.org
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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 | <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 | ||
deletion strains. <br/> <br/> | deletion strains. <br/> <br/> | ||
| + | |||
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/> | 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/> | ||
| - | Environmental stimuli that | + | |
| + | 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/> | ||
| + | |||
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/> | 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/> | ||
| - | NOTE: This map was created solely for picking interesting genes, no annotations | + | |
| + | NOTE: This map was created solely for picking interesting genes, no annotations to ECOCYC were tracked.<br/> <br/> | ||
| + | |||
The CellDesigner model can be <a href="https://2013.igem.org/File:System_Map_(Celldesigner)_(Ecocyc_Only).xml.zip">found here. </a><br/><br/> | The CellDesigner model can be <a href="https://2013.igem.org/File:System_Map_(Celldesigner)_(Ecocyc_Only).xml.zip">found here. </a><br/><br/> | ||
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> | 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> | ||
Revision as of 03:36, 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.
