gravatar for altshs

4 hours ago by

Hi,

I am working on creating a Protein Protein Interaction Network and I am attempting to convert from String ID to the gene name.

I found this as a possible answer for how to convert the two ID forms, but since I am using Neurospora Crassa and not Human models, I had to modify it a bit. This is the code that I used:

library("biomaRt")
listMarts(host = "https://fungi.ensembl.org", port = 443)
test <- c("EFNCRP00000000466", "EFNCRP00000000314", "EFNCRP00000000407", "EFNCRP00000000083")
ensembl_fungi <- useMart(host="https://fungi.ensembl.org", 
                         biomart="fungi_mart", 
                         port = 443,
                         dataset =  "ncrassa_eg_gene")

conversion.table <- data.frame(getBM(attributes = c("ensembl_gene_id","ensembl_peptide_id", "uniprotswissprot", "uniprotsptrembl"),
                                     filters = "ensembl_peptide_id",
                            values = list(test),
                            mart = ensembl_fungi))

This results in an empty data frame. When I put the gene ID’s for each of these (previously known) in as the test and filter by ensembl_gene_id, it says the peptide IDs are: EAA26917, EAA26918, EAA28465, EAA28503, which is very different than what String says the ensembl peptide IDs should be (the original test list).

Does anyone know why this is happening or how to convert from StringID to a gene name directly?

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modified 3 hours ago

by

RamRS26k

written
4 hours ago
by

altshs0



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