Table 1

Reactions and kinetic parameters for the gene expression model
# Chemical reaction(s) Parameters
1 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M1">View MathML</a> ktc=0.0245, τocN(40,42)
2 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M2">View MathML</a> km=150
3 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M3">View MathML</a> ka=150 for n>10, ka=30 for n≤10
4 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M4','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M4">View MathML</a> km=150
5 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M5','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M5">View MathML</a> kp=0.55,τp=3
6 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M6','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M6">View MathML</a> km=150
7 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M7','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M7">View MathML</a> km=150
8 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M8','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M8">View MathML</a> <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M9','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M9">View MathML</a>, τar=100
9 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M10','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M10">View MathML</a> ked=0.009, ded=5
10 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M11','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M11">View MathML</a> kpre=1.9·10−4
11 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M12','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M12">View MathML</a> kpyr=0.75
12 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M13','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M13">View MathML</a> kf=2
13 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M14','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M14">View MathML</a> kdr=0.025
14 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M15','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M15">View MathML</a> ktl=0.53
15 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M16','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M16">View MathML</a> ktrA=35, ktrB=8, ktrC=4.5
16 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M17','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M17">View MathML</a> ktm=10,000
17 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M18','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M18">View MathML</a> see above
18 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M19','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M19">View MathML</a> see above
19 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M20">View MathML</a> kbt=1.5
20 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M21">View MathML</a> kdrop=1.14·10−4
21 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M22','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M22">View MathML</a> ktt is sequence dependent
22 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M23','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M23">View MathML</a> <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M24','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M24">View MathML</a>, τfoldN(420,1002)
23 <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/152/mathml/M25','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/152/mathml/M25">View MathML</a> kdp=0.0029

Chemical reactions, rate constants (in s−1), and delays (in s) used to model transcription and translation. Pro – promoter, Rp – RNA polymerase, Rib – ribosome, [RibR – number of translating ribosomes on RNA strand, P – complete protein, U – unoccupied nucleotide and O – nucleotide occupied by Rp, A – activated nucleotide; UR,OR,AR – corresponding ribonucleotides. n denotes the number of the nucleotide in the sequence. ΔP – range of nucleotides that Rp occupies, ΔP=25. ΔR – range of ribonucleotides that ribosome occupies, ΔR=31. Notation XN(μσ2) denotes that the values of X are drawn from normal distribution with a mean of μand variance of σ2. Parameter values are from measurements in E. coli, mainly for LacZ [3,20,24-34,53]. The duration of protein folding after translation is completed (τfold) is set according to measurements of a commonly used GFP mutant [35].

Emmert-Streib et al.

Emmert-Streib et al. BMC Bioinformatics 2012 13:152   doi:10.1186/1471-2105-13-152

Open Data