KEGG Pathway and ID convertion problem
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Entering edit mode
6 months ago
Bane ▴ 10

Hello there! I am currently having a problem with ID convertion between different databases.

What I did;

I made meta-analyses of Beta vulgaris and found 10 genes with their ENSEMBL ID's. So in order to create KEGG pathways through r package "pathview", converted the ENSEMBL ID's to first ENTREZ ID's through "e-utilities" and then to the KEGG ID's and found 6. So for that purpose, I used NCBI database.

I could not convert KEGG or ENTREZ ID's to KEGG Orthologs through biomart so I used ENSEMBL ID's.

I constructed the pathways that include my genes with pathview through R, and KEGG Mapper through the website and I have different results. Pathview gives me only 1 pathway, which is "bvg00480", but the website gives me 167 pathways which are mostly specie's own pathways.

The main difference there is, I used KEGG Orthologs in KEGG Mapper and KEGG ID's in pathview.

I downloaded the KEGG pathways of Beta vulgaris which includes related KEGG ID's of each pathway and searched my 6 KEGG ID's and only path "00480" related gene was there. With KEGG Orthologs, I found much more pathways.

What can be the problem? Are there really big differences between databases? How can I solve my problem and find the related pathways through pathview?

kegg ensembl entrez pathview • 311 views
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Entering edit mode
6 months ago

Hi Bane,

Apologies if you did this and I poorly understood your question but is your input to pathview entrez ids? You can convert ensembl ids to entrez ids in biomart and then use these entrez ids as input for pathview.

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