Team:TU Munich/Modeling/Priors

From 2012.igem.org

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(Yeast Protein Degradation Rate)
(Yeast Transcription Rate Rate)
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k=fminunc(@(z) sum((y-z(3)*lognpdf(x,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*lognpdf(x,z(1),z(2))).^2),k);
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Revision as of 16:19, 6 September 2012



Contents

Prior Data


Yeast mRNA Degradation Rate


Taken from Wang et. Al 2001

Data was obtained from the Paper (Wang et. Al 2001 [http://www.pnas.org/content/99/9/5860.long]) and processed by [http://arohatgi.info/WebPlotDigitizer/app/] to obtain raw data. Using a least-squared error approximation the distribution of the half life time in was approximated as noncentral t-distribution with parameters μ = 1.769 and ν = 20.59;.

dataGraph = [
0.0018691649126431735,0.0016851538590669062
0.05978099456360327,0.01885629059542104
0.11548146330755026,0.21910551258377348
0.17122389948476902,0.396902157771723
0.2253457470848775,0.4417136917136917
0.2815821076690642,0.3552607791738227
0.3359848142456839,0.249812760682326
0.39216629434020744,0.19272091011221448
0.4465173486912618,0.11490683229813668
0.5026600896166115,0.07854043723608946
0.5569239808370243,0.04735863431515607
0.6111394480959699,0.04208365077930302
0.667233765059852,0.031624075102336016
0.7233280820237343,0.021164499425369035
0.777540321018582,0.017616637181854626
0.8373665112795547,0.010604847561369285
0.8897063570976615,0.008787334874291503
0.9420462029157682,0.006969822187213598
0.9999935434718044,0.005142624707842157
];

X = round(dataGraph(:,1)*90);

y = round(dataGraph(:,2)*2000);

k(1) = 1.769292045467269;
k(2) = 20.589996419308118;
k(3) = 24852.48237036381;

k=fminunc(@(z) sum((y-z(3)*nctpdf(X,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*nctpdf(X,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*nctpdf(X,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*nctpdf(X,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*nctpdf(X,z(1),z(2))).^2),k);

Yeast Protein Degradation Rate


For the Degradation Rate the N-end rule (Varshavsky 1997 [http://openwetware.org/images/c/c2/The_N-end_Rule_Pathway_of_Protein_Degradation.pdf]) served as approximation for the half life time. It states that the half life time in S. cerevisiae can be approximated based on the amino acid after the initial start codon.

Residue ! Half-life
Arg 2 min
Lys, Phe, Leu, Trp, His, Asp, Asn 3 min
Tyr, Gln 10 min
Ile, Glu 30 min
Pro > 5 h
Cys, Ala, Ser, Thr, Gly, Val, Met > 30 h

As these values do not give enough information to infer a proper distribution, only the two lower bounds 5 h and 30 h will serve as approximate lower bounds for the optimization routines.

Yeast Transcription Rate Rate


Pelechano from Wang et. Al 2010

Data was obtained from the Paper (Pelechano et. Al 2010 [http://www.pnas.org/content/99/9/5860.long]) and processed by [http://arohatgi.info/WebPlotDigitizer/app/] to obtain raw data. Using a least-squared error approximation the distribution of the transcription rate was approximated as log-normal distribution' with parameters μ = -1.492 and σ = 0.661;.

dataGraph = [
-1.8,0.3442950751957339
-1.6,1.3525375039897853
-1.4,3.5492668181220783
-1.2,11.28874786429094
-1.0,23.213749272450762
-0.8,26.31522126884587
-0.6,18.273455248681024
-0.4,7.913623476840467
-0.2,3.7755111620134825
0,1.9559339854677913
0.2,0.6458759692833385
0.4,0.12767315671880167
];

x = 10.^dataGraph(:,1);
y = dataGraph(:,2);

k(1) = -0.8;
k(2) = 0.2;
k(3) = 25;

k=fminunc(@(z) sum((y-z(3)*lognpdf(x,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*lognpdf(x,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*lognpdf(x,z(1),z(2))).^2),k);
k=fminunc(@(z) sum((y-z(3)*lognpdf(x,z(1),z(2))).^2),k);


Reference