So noisy,

so good.

Javier Garcia-Bernardo

Computer Science Master Student

Math 303. Complex Networks

Background

Genetic networks

Single input motifs

Downstream Gene Expression

Small fluctuations in Activator

Coordination

$P_{Fixed}(n) =(kAct)^n \\ P_{Pulsing}(n) = \frac{T_{ON}}{T_{ON}+T_{OFF}}\left(kAct\frac{T_{ON}+T_{OFF}}{T_{ON}}\right)^n + \frac{T_{OFF}}{T_{ON}+T_{OFF}}(k0)^n = (kAct)^n\left(\frac{T_{ON}+T_{OFF}}{T_{ON}}\right)^{n-1} \\$ $\begin{align*} &T_{ON} = 120 \\ &T_{OFF} = 120 \\ &Act = 250 \\ \end{align*} \\$

Coordination is good

Noise in Gene Expression

Intrinsic: Affect to only one gene.

E.g. RNApolymerase binding to a promoter

Inherent to the Gillespie Algorithm

Extrinsic: Affect to all genes

E.g. Fluctuations in the levels of the RNApolymerase

Modelled with a Ornstein–Uhlenbeck process

Emergence of Coordination

from noise in gene expression

TATA box example

Lots of genes in stress response in yeast have a TATA box.

Is that advantage due to coordination?

Has noise evolved?

Wow

Conclusions

Small fluctuations in the Activator

coordinate expression of Downstream genes.

Even Infrequent coordination helps to bet-hedge

against sudden changes in the environment.

They do this without cost (Not shown).

Noise can produce the fluctuations.

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