PathVisio doesn't recognise protein identifiers for RAT

[aimee.d...@monash.edu]

Hi there,

I am trying to perform pathway analysis for proteomics data from rat. I have downloaded and connected the Rn_Derby_Ensembl file.

When I try to import the data using UniProt identifiers, PathVisio errors and cannot recognise the identifier.

I separately tried both UniProt name ID (eg. ARK73_RAT) as well as UniProt entry number (eg. P38918) - and selected UniProt-Swissprot as the identifier type 

To check if the problem was with one of the files, I converted the protein IDs to gene IDs (NCBI) to see if it would be recognised with the rat database - it worked - the rat genes are recognised.

Am I selecting the wrong identifier for the protein codes?

Thanks

Aimee

[Martina Summer-Kutmon]

Dear Aimee,

Please use UniProt-TrEMBL as the database. In the species mapping databases that is the database name used for UniProt identifiers. 

Please let me know if that doesn't work.

Best regards,

Tina

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[Aimee Dordevic]

Thanks Tina,

I have tried UniProt-TrEMBL - it also doesn't work

Kind regards

Aimee

[Martina Summer-Kutmon]

Hi Aimee,

Can you provide a couple of rows from the database? Then I can test it.

Best, Tina

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[Aimee Dordevic]

Thanks Tina 

Please see test file attached. You will see both UniProt ID and the entry ID, as well as the corresponding Entrez gene ID. The  Entrez gene ID works with the  Rn_Derby_Ensembl database, but neither of the others are recognised. Let me know if you need anything further

Thank you!

Kind regards

Aimee

[Martina Summer-Kutmon]

Hi Aimee,

Okay, so I found the following: 

With the following selection, 30 of the 50 provided identifiers work fine.

I checked a couple of the identifiers that were not identified (e.g. P11442, P04041). While they are valid identifiers in UniProt, Ensembl does not have any mappings to those identifiers. Our identifier mapping databases are all based on mappings provided from Ensembl. So that is probably the reason why they are not recognized. If the genes are recognized correctly, I think I would use those. 

Hope this clarifies some things.

Best, Tina

To view this discussion on the web visit https://groups.google.com/d/msgid/wikipathways-discuss/93d10f9c-5ca0-424e-ba6a-030a1f1169a9n%40googlegroups.com.