How can I know when a pathway was included in Reactome?
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4.2 years ago
Lluís R. ★ 1.0k

I am interested in a pathway of Reactome, because I would like to use it for a GSEA, however in the Broad Institute the gene set is not in the C2 subcategory of Reactome.
I could only find a reference for this pathway from last July as having "New pathway Illustrations" in the mailing list archive. Also the reactome.db package of Bioconductor doesn't seem to contain it, even if it was updated this April.

How can I know if a pathway is new or not? How can I obtain the gene set of the pathway R-HSA-2559583 ?

reactome • 1.1k views
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Entering edit mode
6 months ago
darklings ▴ 260

2020: Try the ReactomeContentService4R R package interfacing with the newest Reactome database:

To get gene symbols of the pathway R-HSA-2559583:

devtools::install_github("reactome/ReactomeContentService4R")
library(ReactomeContentService4R)
ids <- event2Ids('R-HSA-2559583')
ids[["geneSymbol"]]
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Entering edit mode
4.2 years ago

The genes to pathway membership information is available in the downloadable mapping files. Just select the file with the identifiers that suit you, e.g. for EnsEMBL IDs, use this file.

EDIT: You can also use the pathway browser to navigate to your pathway then select the molecules tab and click on the download button, like here.

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Thanks Jean-Karim, I couldn't find when a certain pathway is included in the database or when a certain compound is included in a pathway in those files. Is this information in the files and I have misread it?

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