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How to find the functions of Reactome pathways?
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15 months ago
Chaimaa • 150

Hello guys, i have found some Reactome pathways from DAVID database and i want to know the functions of these pathways.

Can anyone help me to know their corresponding functions?

I appreciated any help!

Example;

R-HSA-3371568:R-HSA-3371568

R-HSA-445095:R-HSA-445095

R-HSA-3371571:R-HSA-3371571

R-HSA-3371453:R-HSA-3371453

R-HSA-3371511:R-HSA-3371511

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cpad0112 can you plz explain how you did that?

I want to do it one by one and if i want t know if these pathways have any relation to a specific disease how to check that plz?

Appreciated your help!

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In OP data, pathway IDs duplicated and separated by :. Get rid of duplicate values and query NCBI biosystems or reactome. For eg in line "R-HSA-3371568:R-HSA-3371568" is duplicated and remove second or first one so that only one ID remains.

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ok and then how to get its function?

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You can either go to ncbi biosystems or reactome website to search for the IDs. Or programmatically make a construct like:

https://reactome.org/content/query?q=ID1+ID2+ID3+ID4 for URL.

NCBI constuct (with eutils):

$ esearch -db biosystems -query "R-HSA-3371568" | efetch -db biosystems |  xtract -pattern System_names -element System_names_E
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13 months ago
UK, Hinxton, EMBL-EBI

We use the Reactome pathway information for our gene-disease associations in the Open Targets Platform. So you can use this URL to get information on R-HSA-3371568. Change the end of the URL for any other R-HSA ID you like for all the pathways in humans.

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