1. Noise Propagation in Gene Networks
VC Lab, Dept. of Computer Science, NTHU, Taiwan
Juan M. Pedraza and Alexander van Oudenaarden

2. Cyan fluorescent protein
Noise
Fluctuations in concentrations
VC Lab, Dept. of Computer Science, NTHU, Taiwan
Cyan fluorescent protein

3. Schematic design Upstream gene Downstream gene Cascade Promoters
Fluorescent proteins
VC Lab, Dept. of Computer Science, NTHU, Taiwan

4. 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

5. Different manner
VC Lab, Dept. of Computer Science, NTHU, Taiwan

6. Sources of noise Intrinsic noise
Transmitted intrinsic noise from upstream genes
Global noise
VC Lab, Dept. of Computer Science, NTHU, Taiwan

7. Intrinsic noise Low copy numbers of mRNAs
VC Lab, Dept. of Computer Science, NTHU, Taiwan

8. 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

9. Transmitted intrinsic noise
Susceptibility
Logarithmic gain (average expression of j changes when i is varied)
VC Lab, Dept. of Computer Science, NTHU, Taiwan

10. Transmitted intrinsic noise
Susceptibility(Cont.)
Example
VC Lab, Dept. of Computer Science, NTHU, Taiwan

11. 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

12. Noninteracting genes
dominated by the global noise which is transmitted form gene 1 to gene 2
VC Lab, Dept. of Computer Science, NTHU, Taiwan

13. Result
Adding ATC
VC Lab, Dept. of Computer Science, NTHU, Taiwan

14. Result
VC Lab, Dept. of Computer Science, NTHU, Taiwan

15. Discussion Noise-tolerant synthetic circuits in silico v.s. in vivo
VC Lab, Dept. of Computer Science, NTHU, Taiwan

16. 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