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Heat shock response & Petri-net

Explore the heat shock response pathway using a molecular model based on Petri nets at the Computaional Biomodelling Lab, Department of Information Technologies, Åbo Akademi University in Finland. Understand the transcription and protein degradation processes involved, and study the response to stress in the pathway.

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Heat shock response & Petri-net

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  1. Computational Biomodelling Lab. Department of Information Technologies,Åbo Akademi University, 20520 Turku, Finland Heat shock response & Petri-net

  2. The molecular model (Ion Petre et. al) • Transcription • HSF+HSF<->HSF2 • HSF+HSF2<->HSF3 • HSF3+HSE<->HSF3:HSE • HSF3:HSE->HSF3:HSE+HSP • Backregulation • HSP+HSF<->HSP:HSF • HSP+HSF2->HSP:HSF+HSF • HSP+HSF3->HSP:HSF+2HSF • HSP+HSF3:HSE->HSP:HSF+2HSF+HSE • Response to stress • PROT->MFP • HSP+MFP<->HSP:MFP • HSP:MFP->HSP+PROT • Protein degradation • HSP0

  3. o o o HSF HSF2 # of metabolites o o o o o o HSF:HSF2 Petri-net <=> Gene-net place transition Reactions tokens HSF+HSF2->HSF3

  4. k Types of reactions into Petri-net • 2HSF -> HSF2 • HSF3+HSE ->HSF3:HSE • HSP+HSF2->HSP:HSF+HSF • HSF3:HSE->HSF3:HSE+HSP • PROT->MFP (rewriting) • HSP0 (degradation) • HSF+HSF2<-> HSF3 (reverse) 2

  5. o o o o o o o o o transition transition Reaction HSF:HSF2 HSF+HSF2->HSF3 ->HSF+HSF2

  6. translation

  7. A Petri-net for the HSR model 37C 42C

  8. Incidence matrice 10x17

  9. Place invariant, Transition invariant P-invariant: x is a non-zero vector of size n (n=10) T-invariant: y is size of m (m=17)

  10. P-invariant *A P-invariant characterizes a token conservation rule for a set of places *An inv. x is minimal, if any inv. z: supp(z) is not subset of supp(x) - inv. 3 is minimal Deadlock…

  11. trivial T-invariant HS A T-invariant represents a multiset of transitions, which have altogether a zero effect on the marking

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