Table 2

Gene states for erg11 regulation

Iteration


Start

1

2

3

4

Rule


O2[e]

1

1

1

1

1

glucose [e]

1

1

1

1

1

hap1

0

1

1

1

1

O2[e] or not ROX1

rox1

0

0

1

1

1

O2[e] and HAP1

erg11

1

1

1

0

0

O2[e] and HAP1 and (not ROX1)


erg11

1

1

1

1

1

O2[e] and HAP1 and (high_o2 or not ROX1)


To start, all transcription factors are assumed to be "off", and all metabolic genes are "on". The extracellular environment contains only glucose (glucose[e]), oxygen (O2[e]), and essential salts and minerals. Each iteration calculates the next gene state based on the current state of metabolites in the environment and transcription factors. After three iterations, expression of erg11 turns off, unless a modified rule is used that account for high oxygen uptake. The modified rule (shown below the double line) is more consistent with the results in Turi & Loper [25] Rules are taken from the S. cerevisiae regulatory network model iMH805 [16]

Jensen et al. BMC Systems Biology 2011 5:147   doi:10.1186/1752-0509-5-147

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