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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A similar question was recently answered here. When you enter these two IDs:
and choose "From STRING" in drop-down menu, the output will be:
Thanks, it would work to input all of my String IDs into UniProt's ID mapping, does that also help find the UniProt ID's? When I put in the known gene ID's for these two, it outputs a much more in depth result (also containing the UniProt IDs) but not when I just use the StringID's. Here are the known gene ID's for those two String ID's:
That converter is for conversion of ID's from one database to other. If you need additional information then you could use the converted list of ID's for another round?
The
Entrycolumn in the output shown above contains UniProt's ID numbers. Clicking on those links will give you in-depth info, or you can use theDownloadbutton to retrieve all of them in a single file.