Find genes associated with each subsystem in Recon3D model

[yasaman taebi]

Hello,

I want to find list of genes associated with each subsystems in Recon3D model. I used two function in cobratoolbox but they resulted in different subsystem:

1.findsubsysGen(model) resulted in 91 subsystems for 2248 genes in Recon

2.getModelSubsystems(model) resulted in 106 subsystems.

So I am confused in finding genes of each subsystem and appreciate your answer.

Regards

Yasaman

[Farid Zare]

Hi Yasaman,

"getModelSubSystems" returns all the Subsystems exist in a model.

"findSubSysGen" is a special case of "findSubSystemsFromGenes" where it considers all the genes in a model and returns only one subsystem for each gene.

To get the your desired result, I recommend using the following line:

>>[~,singleList] = findSubSystemsFromGenes(model)

The first column of "singleList" represents the genes and the corresponding cells in the second column represents all the associated subsystems.

Best,

Farid