single gene deletion problem

[Mkavscek]

Dear all,

 

I am trying to preform a single gene deletion for my model of Yarrowia lipolytica.

 

I use:

 

model = readCbModel ('model1_5')
model = changeObjective (model, 'LDparticle_SC_e_tp')
sol = optimizeCbModel (model, 'max')

 

 

after running single gene deletion:

 

>> [grRatio,grRateKO,grRateWT,delRxns,hasEffect] = singleGeneDeletion(model,'FBA', model.genes, 'false')

 

I get this:

 

  No Perc       Name Growth rate   Rel. GR
   1    0      Q0045     0.176    53.137
   2    0      Q0105     0.176    53.137
   3    0      Q0250     0.176    53.137
   4    1      Q0275     0.176    53.137
   5    1    YAL023C     0.332   100.000
   6    1    YAL038W     0.332   100.000
   7    1    YAL044C     0.332   100.000
   8    1    YAL062W     0.332   100.000
   9    1 YALI0A02541g     0.332   100.000
  10    1 YALI0A05379g     0.332   100.000
  11    1 YALI0A06655g     0.332   100.000
  12    2 YALI0A09768g     0.332   100.000
  13    2 YALI0A09900g     0.233    70.189
  14    2 YALI0A10659g     0.332   100.000
  15    2 YALI0A11143g     0.233    70.189
  16    2 YALI0A12045g     0.332   100.000
  17    2 YALI0A12353g     0.332   100.000
Error using deleteModelGenes (line 85)
Error: Unexpected MATLAB expression.

 

Error in singleGeneDeletion (line 59)
[modelDel,hasEffect(i),constrRxnNames] = deleteModelGenes(model,geneList{i});

 

 

 

Why does it stop after 17 genes and it does not go further? Does anyone have any idea?

 

 

Another question is what happens with reactions that does not have any gene association?

For that the optKnock is better idea as it turns off each reaction, am I right? Also I would like to know if there is function that would perform double optKnock inplemented in COBRA?

 

 

Thank you very much for your answers!

 

 

With best regards,

 

 

Martin Kavšček

Institute for molecular biosciences

University of Graz

Humboldtstrasse 50, 8010 Graz, Austria

martin.kavscek{at}uni-graz.at

 

 

 

[Ronan M.T. Fleming]

Hi Martin,

what is the output from geneList{18}?

More generally, it is probably a good time for you to start to learn
to use the matlab debugging facilities.
See, for instance http://www.mathworks.de/de/help/matlab/debugging-code.html

You might try entering the following after line 58 of singleGeneDeletion

if i==18
pause
end

Then set a breakpoint (defined in matlab debuging info) at the pause
line, then go in and check what geneList{18} is.

Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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