Team:Toronto/Modeling

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 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.
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 that make references to ECOCYC were made.
The CellDesigner model can be found here.
A .pdf containing the graphic representation can be found here.