ASTD of Drosophila Circadian Clock Model

References

- Li C*, Nagasaki M*, Saito A and Miyano S, Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram, BMC Syst Biol., 4:39, 2010 Apr. (*Equal contributor).

To read and download the paper, please click here.

HFPNe model of Drosophila circadian clock model

Biological diagram of the regulatory mechanism of five genes involved in the Drosophila circadian clock model.

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HFPNe model of circadian rhythm in Drosophila.

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  • The accompanying variable m_x at a place represents the concentration of the corresponding mRNA, protein or the compound. For example, the variable m_1 indicates the concentration of dClk mRNA. Reaction speed (the rate of transcription, translation, complex formation or degradation) is expressed by a simple formula at each transition. For example, the formula m_1/5 indicates the translation rate of dCLK protein that depends on the variable m1 for the dClk mRNA concentration. The real number over an arc is the threshold for the content of the place attached to this arc. For example, the translation of tim mRNA occurs during the period that the place value of tim mRNA exceeds 1.0.
  • Download This Simulation Model:
    • Normal model of wild type: CSML3.0 Version: ZIP | CSML [2009-06-29]
    • Mutant model of dbt^L mutant: CSML3.0 Version: ZIP | CSML [2009-06-29]

Oscillations of tim, per, dClk mRNAs, and the proteins TIM, PER, dCLK, PER/TIM, PER/DBT, dCLK/CYC (left axis) and DBT, CYC (right axis).

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  • Simulation data saved in an expression data format (called EDF). Please use notepad to open it.
    • EDF file of normal model: TSV
    • EDF file of mutant model: TSV

Schematic representation of merged ASTD of ASTD^W and ASTD^L


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The four bold-line blocks of z19, z20, z10 and z11 on the left side show the corresponding temporal subnets that are the minimal sets at respective time points. Dashed-line block shows the state transitions of “z19->z20->z10->z11”in the ASTD and corresponding detailed regulation variations of HFPNe elements. For example, in the structure transformation from z19 to z20, due to the increase in the concentration of PER/TIM, two inhibitory arcs a(p13, t10) and a(p13, t14) are enabled, which results in the deletion of four arcs a(p5, t10), a(p5, t14), a′(t10, p6) and a′(t14, p8). Note that the structure transformation from z11 to z10 is the opposite to the one from z10 to z11.

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Three characterized overviews of the ASTD


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  • (a) Characterized ASTDW and ASTDL with respect to duration (upper) and out-degree (lower).
  • (b) Characterized ASTDWs of the total concentration level difference for per and dClk mRNAs with duration.