mahmoodlab
Reactome Data Source
Hi,
In the documentation, it was mentioned that
"To get the Reactome pathway compositions, refer to PARADIGM"
However the Link is broken. Can you update the link along with the steps to get the pathway compositions.
Alternatively, I have found out a link for downloading the gene associations from the Reactome Website itself (https://reactome.org/download/current/gene_association.reactome.gz). Is this the same as one you had used?
if not , then how do you filter out the pathways that are specific to a particular Organ cancers only (eg. only for Bladder Cancer). Are there some set of steps to follow in general to arrive at a modellable dataset for pathway-gene.
Hoping to get a response @ajv012 @guillaumejaume
It is unfortunate that the link is broken as we used that link while working on this project. Thanks for sharing a replacement link with the community! Another source is the MSigDB website that has a seemingly large number of pathway-sets that can be used.
We do not select pathways that are specific to any organ or only cancer/ non-cancer pathways. we selected pathways that had sufficient number of gene expression data.
