Table 1.

Reactions and rate parameters used in the S. cerevisiae gene expression model.

Description	Reaction	Stochastic rate [s−1]	Defined regions
Inducer/TF binding	${\mathrm{I}}_{\text{in}}+{\mathrm{D}}_{\text{off}}\stackrel{k_{\text{gnOn}}}{\to }{\mathrm{D}}_{\text{on}}$	1.599	Nucleoplasm
Transcription	${\mathrm{D}}_{\text{on}}\stackrel{k_{\text{ts}}}{\to }{\mathrm{D}}_{\text{on}}+\mathrm{m}$	6.202 × 10−3	Nucleoplasm
SSU/mRNA association	$\mathrm{R}+\mathrm{m}\stackrel{k_{\text{tlInit}}}{\to }\mathrm{R}:\mathrm{m}$	7.043 × 103	Ribosome
Translation elongation	$\mathrm{R}:\mathrm{m}\stackrel{k_{\text{tlTerm}}}{\to }\mathrm{R}+\mathrm{m}+\mathrm{T}$	1.393	Ribosome
mRNA degradation	$\mathrm{m}\stackrel{k_{\text{mDcy}}}{\to }\text{Ø}$	7.889 × 10−4	Nucleoplasm, Ribosome, NPC, Cytoplasm
mRNA degradation	$\mathrm{R}:\mathrm{m}\stackrel{k_{\text{mDcy}}}{\to }\mathrm{R}$	7.889 × 10−4	Ribosome
Transcription (other)	$\text{Ø}\stackrel{k_{\mathrm{t}{\mathrm{s}}^{\prime }}}{\to }{\mathrm{m}}^{\prime }$	5.895 × 10−5	Nucleoplasm
SSU/mRNA association (other)	$\mathrm{R}+{\mathrm{m}}^{\prime }\stackrel{k_{\text{tlInit}}}{\to }\mathrm{R}:{\mathrm{m}}^{\prime }$	7.043 × 103	Ribosome
Translation elongation (other)	$\mathrm{R}:{\mathrm{m}}^{\prime }\stackrel{k_{\text{tlTer}{\mathrm{m}}^{\prime }}}{\to }\mathrm{R}+{\mathrm{m}}^{\prime }$	1.101	Ribosome
mRNA degradation (other)	${\mathrm{m}}^{\prime }\stackrel{k_{\text{mDc}{\mathrm{y}}^{\prime }}}{\to }\mathrm{Ø}$	5.776 × 10−4	Nucleoplasm, Ribosome, NPC, Cytoplasm
mRNA degradation (other)	$\mathrm{R}:{\mathrm{m}}^{\prime }\stackrel{k_{\text{mDc}{\mathrm{y}}^{\prime }}}{\to }\mathrm{R}$	5.776 × 10−4	Ribosome
Passive diffusional transport	${\mathrm{I}}_{\text{in}}\stackrel{k_{\text{txDif}}}{\to }{\mathrm{I}}_{\text{out}}$	2.33 × 10−3	Membrane
Passive diffusional transport	${\mathrm{I}}_{\text{out}}\stackrel{k_{\text{txDif}}}{\to }{\mathrm{I}}_{\text{in}}$	2.33 × 10−3	Membrane
Transporter/inducer association	$\mathrm{T}+{\mathrm{I}}_{\text{out}}\stackrel{k_{\text{txOn}}}{\to }\mathrm{T}:\mathrm{I}$	2.134	Membrane
Active inducer transport	$\mathrm{T}:\mathrm{I}\stackrel{k_{\text{tx}}}{\to }\mathrm{T}+{\mathrm{I}}_{\text{in}}$	12.000	Membrane
Transporter/inducer dissociation	$\mathrm{T}:\mathrm{I}\stackrel{k_{\text{txOff}}}{\to }\mathrm{T}+{\mathrm{I}}_{\text{out}}$	0.120	Membrane
Transporter degradation	$\mathrm{T}\stackrel{k_{\text{tDcy}}}{\to }\text{Ø}$	2.567 × 10−4	Cytoplasm, Membrane
Transporter degradation	$\mathrm{T}:\mathrm{I}\stackrel{k_{\text{tDcy}}}{\to }\text{Ø}$	2.567 × 10−4	Cytoplasm, Membrane