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?