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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