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Noise Propagation in Gene Networks
VC Lab, Dept. of Computer Science, NTHU, Taiwan Juan M. Pedraza and Alexander van Oudenaarden
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Cyan fluorescent protein
Noise Fluctuations in concentrations VC Lab, Dept. of Computer Science, NTHU, Taiwan Cyan fluorescent protein
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Schematic design Upstream gene Downstream gene Cascade Promoters
Fluorescent proteins VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Quantify Correlation Self-correlations(variation) Cross-correlations
F: fluorescence levels i, j: indices refer to the gene number Self-correlations(variation) Cross-correlations , , VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Different manner VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Sources of noise Intrinsic noise
Transmitted intrinsic noise from upstream genes Global noise VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Intrinsic noise Low copy numbers of mRNAs
VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Transmitted intrinsic noise
Three factors Intrinsic noise for upstream gene The effect of temporal averaging(depends on the lifetimes of the proteins) Susceptibility of the downstream gene to the upstream one VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Transmitted intrinsic noise
Susceptibility Logarithmic gain (average expression of j changes when i is varied) VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Transmitted intrinsic noise
Susceptibility(Cont.) Example VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Global noise Cellular components change the reaction rate
Transmitted global fluctuation does not simply add to the direct global noise (because they are from same source) VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Noninteracting genes dominated by the global noise which is transmitted form gene 1 to gene 2 VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Result Adding ATC VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Result VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Discussion Noise-tolerant synthetic circuits in silico v.s. in vivo
VC Lab, Dept. of Computer Science, NTHU, Taiwan
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Reference Tom Ellis, Xiao Wang & James J Collins, Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nature Biotechnology 27, (2009) VC Lab, Dept. of Computer Science, NTHU, Taiwan
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