Table 1 Processes included in the HOM2 genetic circuit description

Repressor binding

\(\mathrm {D}^{1}_{00} + \mathrm {P}^{2}_{2} \underset {q_{12}}{\overset {k_{12}}{\rightleftharpoons }} \mathrm {D}^{1}_{10}\)

\(\mathrm {D}^{2}_{00} + \mathrm {P}^{1}_{2} \underset {q_{22}}{\overset {k_{22}}{\rightleftharpoons }} \mathrm {D}^{2}_{10}\)

\(\mathrm {D}^{1}_{10} + \mathrm {P}^{2}_{2} \underset {q_{14}}{\overset {k_{14}}{\rightleftharpoons }} \mathrm {D}^{1}_{20}\)

\(\mathrm {D}^{2}_{10} + {P^{1}_{2}} \underset {q_{24}}{\overset {k_{24}}{\rightleftharpoons }} \mathrm {D}^{2}_{20}\)

RNAp binding

\(\mathrm {D}^{1}_{00} + \mathrm {R} \underset {q_{13}}{\overset {k_{13}}{\rightleftharpoons }} \mathrm {D}^{1}_{01}\)

\(\mathrm {D}^{2}_{00} + \mathrm {R} \underset {q_{23}}{\overset {k_{23}}{\rightleftharpoons }} \mathrm {D}^{2}_{01}\)

\(\mathrm {D}^{1}_{10} + \mathrm {R} \underset {q_{15}}{\overset {k_{15}}{\rightleftharpoons }} \mathrm {D}^{1}_{11}\)

\(\mathrm {D}^{2}_{10} + \mathrm {R} \underset {q_{25}}{\overset {k_{25}}{\rightleftharpoons }} \mathrm {D}^{2}_{11}\)

\(\mathrm {D}^{1}_{20} + \mathrm {R} \underset {q_{17}}{\overset {k_{17}}{\rightleftharpoons }} \mathrm {D}^{1}_{21}\)

\(\mathrm {D}^{2}_{20} + \mathrm {R} \underset {q_{27}}{\overset {k_{27}}{\rightleftharpoons }} \mathrm {D}^{2}_{21}\)

Transcription initiation

\(\mathrm {D}^{1}_{01} \overset {\alpha _{1m}}{\rightarrow } \mathrm {E}^{1} + \mathrm {D}^{1}_{00}\)

\(\mathrm {D}^{2}_{01} \overset {\alpha _{2m}}{\rightarrow } \mathrm {E}^{2} + \mathrm {D}^{2}_{00}\)

\(\mathrm {D}^{1}_{11} \overset {\alpha _{1m}}{\rightarrow } \mathrm {E}^{1} + \mathrm {D}^{1}_{10}\)

\(\mathrm {D}^{2}_{11} \overset {\alpha _{2m}}{\rightarrow } \mathrm {E}^{2} + \mathrm {D}^{2}_{10}\)

\(\mathrm {D}^{1}_{21} \overset {\alpha _{1m}}{\rightarrow } \mathrm {E}^{1} + \mathrm {D}^{1}_{20}\)

\(\mathrm {D}^{2}_{21} \overset {\alpha _{2m}}{\rightarrow } \mathrm {E}^{2} + \mathrm {D}^{2}_{20}\)

Elongation

\(\mathrm {E}^{1} \overset {\alpha _{1m}^{\prime }}{\rightarrow } \mathrm {M}^{1} + \mathrm {R} \)

\(\mathrm {E}^{2} \overset {\alpha _{2m}^{\prime }}{\rightarrow } \mathrm {M}^{2} + \mathrm {R} \)

Translation

\(\mathrm {M}^{1} \overset {\alpha _{1p}}{\rightarrow } \mathrm {P}^{1} + \mathrm {M}^{1} \)

\(\mathrm {M}^{2} \overset {\alpha _{2p}}{\rightarrow } \mathrm {P}^{2} + \mathrm {M}^{2} \)

Dimerization

\(\mathrm {P}^{1} + \mathrm {P}^{1} \underset {q_{11}}{\overset {k_{11}}{\rightleftharpoons }} \mathrm {P}^{1}_{2}\)

\(\mathrm {P}^{2} + \mathrm {P}^{2} \underset {q_{21}}{\overset {k_{21}}{\rightleftharpoons }} \mathrm {P}^{2}_{2}\)

Degradation

\(\mathrm {M}^{1} \overset {\gamma _{1m}}{\rightarrow } \oslash \)

\(\mathrm {M}^{2} \overset {\gamma _{2m}}{\rightarrow } \oslash \)

\(\mathrm {P}^{1} \overset {\gamma _{1p}}{\rightarrow } \oslash \)

\(\mathrm {P}^{2} \overset {\gamma _{2p}}{\rightarrow } \oslash \)

\(\mathrm {P}^{1}_{2} \overset {\gamma _{1p}/\sigma _{1}}{\rightarrow } \oslash \)

\(\mathrm {P}^{2}_{2} \overset {\gamma _{2p}/\sigma _{2}}{\rightarrow } \oslash \)