This is a test version of Biostars. For the public version, visit https://www.biostars.org.
convert Gene ID to Gene Symbol

Can anyone suggest how can I change Gene Id to Gene symbol in a csv file of a dataset of rna seq

gene-id
• 1,290 views • link
updated by pinheirofabiano • pinheirofabiano • written by majorprogeria • majorprogeria

Always show examples of ID's (and include the source/genome) when asking questions about them. Otherwise there is no way to find out what you are working with.

That said, if these came out of a GTF file there may be a different field that may contain the Gene Symbols you need.

• 0 views • link
written by GenoMax GenoMax

this one of the example

"customerID
# uniSp.2
# uniSp.4
# uniSp.5
hsa-let-7a-3p
hsa-let-7a-5p
hsa-let-7b-3p"

and another one is this

"GeneID
100287102
653635
102466751
107985730
100302278
645520"
• 0 views • link
updated by GenoMax GenoMax • written by majorprogeria • majorprogeria

Using EntrezDirect (LINK) you can look these up at NCBI:

$ esearch -db gene -query "hsa-let-7a-3p" | esummary | xtract -pattern DocumentSummary -element Id,NomenclatureSymbol 
406881  MIRLET7A1
406883  MIRLET7A3

and

$ esearch -db gene -query "653635" | esummary | xtract -pattern DocumentSummary -element Id,NomenclatureSymbol            
653635  WASH7P

Not sure what the first part about Customer ID is but the second set appears to be Entrez ID's.

• 0 views • link
written by GenoMax GenoMax

1 answer

I asked the same question months ago...

gene ID to gene symbol in R

• 0 views • link
written by pinheirofabiano • pinheirofabiano

Log in to answer this question.

More posts like this