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Question: Indirect path in KEGG, activation or inhibition?
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gravatar for haoran.chen
9 months ago by
haoran.chen0 wrote:

Hi guys,

I'm working on KEGG data recently. And I noticed that there is a kind of "indirect path" without specific label for activation or inhibition.

For instance, in PI3K-Akt pathway http://www.genome.jp/kegg-bin/show_pathway?hsa04151, PI3K-PIP3-Akt path is an path with "indirect" label in KEGG data because KEGG data does not contain chemical compounds such as PIP3, so is PTEN-PIP3-Akt. But these two paths present different effects, i.e. activation from PI3K to Akt and inhibition from PTEN to Akt. However, we cannot differentiate them just based on data, so I have to manually set up activation and inhibition labels for them respectively. Do we have a way to determine if a indirect path in KEGG data is activation or inhibition?

Thank you,

Haoran

ADD COMMENTlink modified 9 months ago by gabriele.sales70 • written 9 months ago by haoran.chen0
1
gravatar for gabriele.sales
9 months ago by
European Union
gabriele.sales70 wrote:

Dear Haoran,

this is a good observation. Right now graphite is not able to reconstruct the "sign" of the reaction when it goes through a compound, like PIP3 here. It would be nice to do that, however. We'll try to implement this behaviour in a new release.

 

Best,

  Enrica & Gabriele

ADD COMMENTlink modified 9 months ago • written 9 months ago by gabriele.sales70

Dear Enrica & Gabriele,

Thank you so much for your prompt reply! Could you please inform me the date of the next release?

Thanks again,

Haoran

ADD REPLYlink written 9 months ago by haoran.chen0

We will release a new version of graphite with the next Bioconductor release, which should take place mid-April.

 

Best,

  Gabriele
 

ADD REPLYlink written 9 months ago by gabriele.sales70

Thank you Gabriele!

Best,

Haoran

ADD REPLYlink written 8 months ago by haoran.chen0
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