finding blocked pathways

[Uri David Akavia]

Hi.

I'm reviewing a modification I made of RECON 2.2, and I'm wondering about blocked reactions.

Some reactions stand alone, and unblocking them will only unblock one reaction. Some reactions are pathways - for example, the modified model couldn't produce HMG-CoA, which meant that the entire cholesterol synthesis pathway was blocked. I figured this out by looking at the reactions and reviewing biology, but I'm wondering if there is a computational way to prioritize pathways.

I'll give two toy examples of a series of blocked reactions

A ---> B

C ---> D ---> E ----> F ----> G

In the first case, fixing this reaction will only solve one.

In the second case, if C is not produced, then at least 4 reactions are blocked. It also means that looking at D, E, F is potentially a waste of time, because even if those reaction is perfect, they will still be blocked.

I'd like to prioritize chains of multiple blocked reactions and focus on them, because the biological review can take a long time.

I've tried using findBlockedReactions, findNeighborReactions and finding gaps or dead ends, but I can't seem to combine them in the way I want. Can I use graph connectivity properties for this?

I feel like someone has published an algorithm about that, but I'm not sure. Any suggestions?

Thanks,

Uri David

[Ines Thiele]

Hi Uri

Is there a particular reason why you use Recon2.2 instead of Recon 3?

Ines

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[Uri David Akavia]

Hi Ines,

I started working on RECON 2.2 before RECON3 was published, and I'm wrapping it up now. I don't want to redo my work on RECON 3D.

Any suggestions on prioritizing blocked reactions?

Uri David

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[Ronan M.T. Fleming]

Hi Uri,

you could try forcing a reaction to be active that is blocked, then try to find if relaxing a minimal number of bounds can unblock it. 

https://opencobra.github.io/cobratoolbox/latest/tutorials/tutorialRelaxedFBA.html

Regards,

Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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[Andres Mauricio Pinzon Velasco]

Dear Dr. Fleming,
In the tutorial you just cited there is a citation to a work entitled: "Cardinality optimisation in constraint-based modelling: Application to Recon 3D ", but I have not been able to find it, is this still under revision or can I find it in a specific place?
Regards,

Andrés M. Pinzón Ph.D.

AssociateProfessor

Head of the Master Program in Bioinformatics

Group Leader - Bioinformatics and Systems Biology

Instituto de Genética - Universidad Nacional de Colombia

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