Apple gene ID conversion tool

Question

[rj.rezwan]

Hi,

I am converting the gene IDs of apple, e.g., MDP0000006982, MDP0000007682, MDP0000799306,MDP0000799753, into entrez ID and ensemble gene ID using R bioconductor package "mygene", but function "queryMany" has not been working and giving error continuously.

Does anyone help me how to convert these IDs, please suggest any suitable tool or how can I fix the above-mentioned issue?

Thanks

[WouterDeCoster]

function "queryMany" has not been working and giving error continuously.

Please be as complete as possible and show us the code you used and the errors you get.

[rj.rezwan]

library(mygene)

genesid <-  c('MDP0000938167','MDP0000746295','MDP0000690401','MDP0000585568','MDP0000450178','MDP0000315706','MDP0000305723')

queryMany(genesid, scopes="locus_ID", fields=c("uniprot", "entrez", "ensembl.gene"), species="apple")

[GenoMax]

Those gene ID's appear to be exclusively used by Apple genome database. Ensembl does not contain apple genome so is likely to not have Ensembl gene ID's. NCBI's apple genome does not use these ID's either. Unless someone has done the work upfront you may need to assign these by doing some blasting yourself.

[lieven.sterck]

Not 100% sure but it might be worth to have a look at PLAZA , they certainly host the apple genome and they often do a lot of work for geneID conversions (perhaps you need to go through different version of PLAZA to get the exact dataset you want )

[sangi]

Thank you, Lieven. Tried all the dicot versions for Malus in PLAZA, I found that it only displays the list as a Homolog and Ortholog couldn't find the conversion from like MD00G1000100 to EnterZ ID (103435615) or LOC103435615.

[lieven.sterck]

Yes, I noticed similar indeed. Did you check the download sections as well? There is a directory called conversion of such, it should contain lists of geneIDs (but once more it's possible they are just not available for malus :/ )

[sangi]

Thank you. Finally, I was able to get a file with Arabidopsis and MD gene sets. I merged multiple files to get the ENTERZID.

[GenoMax]

Not sure if this is the file you are referring to but those are Arabidopsis homologs. I don't see how you could have got entrezID that corresponded with your original apple identifiers.

[sangi]

Hi rj.rejwan Can you please share how you did it? I am having the same problem.