Suppose, We have a parent pathway 'Autophagy' (a top-level pathway in Reactome database) which has the stable id: R-HSA-9612973.2. This pathway has three sub-pathways: Macroautophagy (R-HSA-1632852.8), Chaperone Mediated Autophagy (R-HSA-9613829.3) & Late endosomal microautophagy (R-HSA-9615710.3).
Is there any way of removing two of those sub-pathways and get the rest one? In other words, can I remove Chaperone Mediated Autophagy (R-HSA-9613829.3) & Late endosomal microautophagy (R-HSA-9615710.3) sub-pathways from Autophagy (R-HSA-9612973.2) pathway in order to get only the Macroautophagy (R-HSA-1632852.8) sub-pathway?
What will be the right thing to do that? I have only the hierarchy information and the list of genes associated with the pathways. I can remove those genes, but how can I remove the edges/connections between them? In reactome, I suppose each edge also represents reactions.
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Muiz Khan •
1 answer
I am not sure what you mean by "remove" this pathway. In ReactomeGSA, for ssgsea analysis you are able to include a list of pathways: "A comma delimited list of pathways to include in the analysis. All other pathways will be ignored." Maybe this is useful for you?
Perhaps you can provide more details & email the Reactome helpdesk for more support: help@reactome.org
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