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

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