Missing Pathway

[Marta Correia]

Dear all,

I've been working on a gene list that was compiled having in account a set of metabolic pathways found in Wikipathways. The gene list was built between September 2018 and April 2019. Meanwhile, I have a table with the genes of my list and the correspondent pathways, and I would like to add the respective Wikipathways page link to each of the pathways name. However, I realized that one of these pathways is no longer available in Wikipathways, neither in the archives.

After searching by its full name without success, I try to find the pathway adding its ID to the url (https://www.wikipathways.org/index.php/Pathway:WP2764), but it shows me the following result:

'This pathway doesn't exist, you can search for the pathway you are looking for or create a new pathway.'

The pathway in question is the following: 'Lipid digestion, mobilization and transport' (WP2764), for Homo sapiens, version active in 20/09/2018.

I've searched in GeneCards for one of the genes present in this pathway (https://www.genecards.org/cgi-bin/carddisp.pl?gene=PNLIPRP2), and in the results sub-section "Pathways & Interactions" it appears the 'missing pathway' with a link to Reactome (https://reactome.org/PathwayBrowser/#/R-HSA-73923), but this link fails to load completly...

Thanks in advance,

Best,

Marta

[Alex Pico]

Hi Marta,

I searched the archive for 20180910 as well and did not find it. We don’t change our archived files, so if it’s not there today, then it was not there in 2018. 

An important note, however, is that we only archive the “approved” pathways each month. Perhaps WP2764 never met approval and was eventually deleted for lack of interest in completing it?

If this is the case, then I don’t think we have a copy of it anymore.  

 - Alex

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[Martina Summer-Kutmon]

Dear Marta,

Yes, this pathway was a Reactome pathway. Sometimes Reactome decides to merge or split up pathways. In this case, I think they split the pathway into several other pathways (e.g. Digestion / Absorption). Those are also both available in WikiPathways:

https://www.wikipathways.org/index.php/Pathway:WP4104 

https://www.wikipathways.org/index.php/Pathway:WP4035

I couldn't quickly find the release notes to see when the pathway was removed but you could check with Reactome directly. 

Not sure if that is feasible for your situation but you could create an updated list of pathways for your gene list with the R package (see attached example script). Then you would have up-to-date pathway information. 

Best regards,

Tina

To view this discussion on the web visit https://groups.google.com/d/msgid/wikipathways-discuss/3F20C4E7-0449-43EB-AA31-243628BD5583%40gladstone.ucsf.edu.

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com

[Marta Correia]

Thanks both of you!

I will check that information with Reactome and take a look in the R script.

Best,

Marta