how to find flux of gene ??

[Venkata Sri Krishna Kona]

Dear COBRA User,

Well we know that model consists Rxn and for Rxns we do have lb and ub values. My query is when i would like to generate visual graphs on www.proteomaps.net i need to enter two values those are gene and its fluxes 

Like for example 

Here b0002 is a gene and adjacent to it some value of 4183640 is mentioned   .....How can we generate such data  by any function in cobratoolbox/matlab

[Almut Heinken]

Hello,
may you clarify what data exactly you are trying to generate? I believe for this tool, you need proteomics data.
Best regards

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[Venkata Sri Krishna Kona]

Hello there

Here i would like to generate data/flux of genes so as i can create beautiful graphs in www.proteomaps.net  after simulating my model in  Cobratoolbox , I hope we are aware that there are 1356 genes in 'iEC1356_Bl21DE3' model ...that implies ecoli produces 1356 proteins. Now with which function in cobratoolbox we can see/generate Flux value of gene a.k.a protein. 

FYI : Flux is generated only for Rxns not for gene by performing "FBAsolution = optimizeCbModel(model)" 

 

[Almut Heinken]

Hi,

I see, so you want to have one flux value per protein. You can get the reactions encoded by each gene from mining the gene-protein-reaction associations (using the findRxnsFromGenes function). However, there are often more than one reaction per gene so you do not get one unique value per protein. Maybe someone from the community has another suggestion.

Best regards,

Almut

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[Venkata Sri Krishna Kona]

Hello Cobra-Toolbox  User

I received below revert from protemaps.net website regard same query i.e how to see flux value of gene instead of Rxns ub or lb .....

If I understand you correctly, you have flux data and would like to visualise them on a proteomap. I think this means bending the method a bit, because flux data refer to chemical reactions and and the proteomaps refers to genes (ORF or gene IDs for specific organisms, or KO numbers for classes of orthologous genes).

The problem is that in general, the relation between enzyme-catalysed reactions and genes is not one-to-one. For E coli, you will find information about this (sometimes simple, sometimes complicated) relation in the EcoCyc database (https://www.ecocyc.org/).

If you're looking for a pragmatic solution, and if smaller inaccuracies are acceptable for you, you could could create a mapping between your reactions and E coli gene IDs by mapping the reactions in your flux solution to reaction identifiers that exist in EcoCyc, use EcoCyc to find the "most pertinent" gene related to a reaction. Another possibility is to use an E coli metabolic model (e.g. the iML1515 model) that already contains information about reaction-gene mappings. But also in this case, the mappings will not be one-to-one, so you will have to make your own (to an extent, arbitrary) decisions.

===

Now after reading above response from proteomaps.net author, i request cobratoolbox users to suggest me possible action i can take to see arbitatory values of Gene...  If someone provide code that would be really grateful. 

[Almut Heinken]

Hello Venkata,

I believe the type of plot you are trying to generate is called a Voronoi treemap. I think it might be easier for you to find another tool that can generate these plots with more customizable inputs. Then you could use the reaction fluxes directly and the reaction subsystems as annotations for weighing the partitions.

Best regards,

Almut

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