The meaning of output parameters of FSEOF

[ZhendongZhang-Synbio]

After I ran FSEOF and exported a xls file, I get the vision below:

I wonder what's the meaning of the slope and direction

thank you!🌹

[ZhendongZhang-Synbio]

well I see the answer in https://github.com/SysBioChalmers/RAVEN/issues/220

and now I want to know how to confirm the target genes(or what we say key genes)? By the Gr Rule? all of the genes is the key gene to delete or overexpress?

[ZhendongZhang-Synbio]

any good guys answer me?😥

[haowang-bioinfo]

I wonder what's the meaning of the slope and direction

the FSEOF method explores reactions that suppose to co-upregulated together with the one for target formation.

The slope value indicates the times of flux change when assuming that the target formation flux has 1 unit of flux increase.

The direction value is associated with the reversibility of reactions: 0 irreversible reactions; 1 reversible reaction, flux has been consistently increasing in forward direction; -1 reversible reaction, flux has been consistently increasing in reverse direction. Note that the reactions with mixed forward and reverse fluxes in the iterations (10 iterations by default) are excluded from the results.

[ZhendongZhang-Synbio]

thank you @haowang-bioinfo

and now I want to know how to confirm the target genes(or what we say "key genes")? By the Gr Rule? all of the genes are the key genes we can delete or overexpress?

[ZhendongZhang-Synbio]

hello？

[JonathanRob]

@ZhendongZhangSCAU I don't think that the model/simulations will be able to tell you much more beyond which genes are of interest. Once you obtain the "key genes", then I would suspect that the next best step is to manually investigate the literature/gene databases for further biological details on these genes, and identify which genes should be targeted for deletion or overexpression in followup experiments.

[haowang-bioinfo]

By the Gr Rule? all of the genes are the key genes we can delete or overexpress?

FSEOF predicts co-upregulated reactions with target formation one, therefore the genes in the reported grRules suppose to be key genes to overexpress. @JonathanRob made a good point here that it's better to check literature/database before actual experimental verification.

[ZhendongZhang-Synbio]

Thank you for your valuable answers.🌹 @JonathanRob @haowang-bioinfo I'm sorry I'm busy with other academic activities recently and didn't reply in time.

the genes in the reported grRules suppose to be key genes to overexpress.

I and other researchers will carefully consult the relevant literature and databases before the specific 'wet experiment'.