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reactome / ReactomeGSA

R client for the REACTOME Analysis Service for comparative multi-omics gene set analysis
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pathway hierarchy for annotating pathways #48

Open bravedu01 opened 3 years ago

bravedu01 commented 3 years ago

Pathway analysis become hard to interpret when we obtain a tons of differential pathways. In this scenario, grouping the pathways into different categories and showing the top n in each category may be a good choice.

This is because a subset of genes can be shared by many similar pathways such as some metabolic pathways. That means we could group these pathways to simply the pathway description and make people easy to understand.

For an easier reachable source for the analysis in R, a table of pathway hierarchy would be highly helpful to annotate which category(metabolism, inflammation) a pathway belongs to. Do you have a link to download this table? Thanks a lot

jgriss commented 3 years ago

Hi @bravedu01

Thanks a lot for the feedback!

You can find the pathway structure in Reactome's download area: https://reactome.org/download-data

The direct link to the pathway relations is here: https://reactome.org/download/current/ReactomePathwaysRelation.txt

We will test whether we can integrate this somehow into the ReactomeGSA package.

Kind regards, Johannes

jcasadogp commented 3 months ago

Hello,

Is there any improvement in this?

I have the following DF and I would like to add the pathway hierarchy to it:

head(pathway2name)
          PATHID                                      PATHNAME
          <char>                                        <char>
1: R-HSA-1059683         Homo sapiens: Interleukin-6 signaling
2:  R-HSA-109581                       Homo sapiens: Apoptosis
3:  R-HSA-109582                      Homo sapiens: Hemostasis
4:  R-HSA-109606 Homo sapiens: Intrinsic Pathway for Apoptosis
5:  R-HSA-109703             Homo sapiens: PKB-mediated events
6:  R-HSA-109704                    Homo sapiens: PI3K Cascade

Also, @jgriss you provided a link to the pathway relations, but I don't really get if those are the pathways with their hierarchies.

Thank you very much,

Julia

jcasadogp commented 3 months ago

Also, this list from the Reactome documentation containing the relation between pathway names and their top level pathway is not completed. Do you know where can I get the complete one?