sri international bioinformatics 1 regulation in pathway tools pathway tools workshop august 2009
TRANSCRIPT
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Regulation in Pathway Tools
Pathway Tools Workshop
August 2009
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What can be regulated?
Gene transcription Transcription initiation Transcription termination (attenuation) Sigma factors
mRNA translationSubstrate-level regulation of enzymes
Allosteric Competitive
A ligand binding to a protein can activate or inactivate it
Protein degradationOther…
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The Regulation Class Taxonomy Regulation-of-Enzyme-Activity Regulation-of-Gene-Products
Regulation-of-Degradation Regulation-of-Production
Regulation-of-Reactions Regulation-of-Transcription
Regulation-of-Transcription-Initiation Transcriptional-Attenuation
Protein-Mediated-Attenuation Rho-Blocking-Antitermination Ribosome-Mediated-Attenuation RNA-Mediated-Attenuation RNA-Polymerase-Modification Small-Molecule-Mediated-Attenuation
Regulation-of-Translation RNA-Mediated-Translation-Regulation Protein-Mediated-Translation-Regulation
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Regulation Statistics for EcoCyc
Transcription Initiation: 2551 regulatory interactions, covering 851 transcription units
Attenuation : 18 regulatory interactions (16 TUs) Ribosome-mediated: 11 Protein-mediated: 4 Small-molecule-mediated: 1 Rho-blocking: 1
Translation: 51 regulatory interactions (41 TUs) RNA-mediated: 32 Protein-mediated: 16
Enzyme substrate-level regulation: 2431 regulatory interactions (579 enzymes)
Regulation of reactions: 20 regulatory interactions
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Display of Transcriptional Regulation
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Editor for Transcription Initiation
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Editor for Transcription Attenuation
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More Example Displays…
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Integrating Regulatory Information
Now that we have individual regulatory interactions, we can: Show all regulatory interactions that affect a gene Incorporate regulation into pathway displays
substrate-level enzyme regulation and feedback inhibition regulators of genes involved in pathway transcription units regulated by signaling pathway
When we look at an object, see everything it regulates transcription factor RNA polymerase RNA small molecule
Highlight regulated reactions on cellular overview diagram Regulatory Overview Diagram
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Regulation section of L-tryptophan display