Get gene names from ensembl ID or gene region

Question

[L. A. Liggett]

I have some RNASeq data that has fpkm values labeled with genome positions like chr7 52823165 52830546 Ensembl IDs like ENSMUST00000143813 and gene symbols like 0610005C13Rik. Is there a good programmatic way in python to get gene names from any of this data so I can match up the fpkm values with the actual altered genes?

[GenoMax]

This is the mouse genome so you should be able to use the answer posted a couple of days back here : A: How to add gene symbol to RNA-Seq data using R

Answer 1

[Alex Reynolds]

You could use Python mygene with the ensembl.transcript scope:

#!/usr/bin/env python

import sys
import mygene

mg = mygene.MyGeneInfo()

names = []
for line in sys.stdin:
    names.append(line.rstrip())

for name in names:
    result = mg.query(name, scopes="ensembl.transcript", fields=["symbol"], species="mouse", verbose=False)
    ensembl_name = name
    for hit in result["hits"]:
        if "symbol" in hit:
            sys.stdout.write("%s\t%s\n" % (ensembl_name, hit["symbol"]))

Given a text file like names.txt:

ENSMUST00000143813
ENSMUST00000099042
ENSMUST00000073363

You could run this script like so:

$ ./map_ensembl_transcripts_to_hgnc_symbols_mm10.py < names.txt
ENSMUST00000143813      0610009L18Rik
ENSMUST00000099042      Gm10717
ENSMUST00000073363      Amtn

Installation instructions: https://pypi.org/project/mygene/

Full listing of scopes/fields here: http://docs.mygene.info/en/latest/doc/query_service.html#available-fields

Edit: If you have a lot of genes/transcripts/etc. in names.txt, then you may instead want to use querymany(), which queries all genes/transcripts/etc. at once, instead of running one query() call per gene/transcript/etc.:

#!/usr/bin/env python

import sys
import mygene

mg = mygene.MyGeneInfo()

names = []
for line in sys.stdin:
    names.append(line.rstrip())

results = mg.querymany(names, scopes='ensembl.transcript', fields='symbol', species='mouse', verbose=False)
for res in results:
    if 'symbol' in res:
        sys.stdout.write("%s\t%s\n" % (res['query'], res['symbol']))

Answer 2

[cilgaiscan]

Hey! I use biomaRt in R. Here is my code for it. Hope it will help :

library("biomaRt")  
differentialexpression <- read.csv("put your file's path here", sep = ",",header = T)
ensembl = useMart("ensembl", dataset="mmusculus_gene_ensembl")
values<- differentialexpression$columnnameensembl 
data <- getBM(attributes=c("ensembl_gene_id", "hgnc_symbol"), filters = "ensembl_gene_id", values = values, mart= ensembl)

Answer 3

[Eric Lim]

Their REST is probably the quickest, especially for single ID/gene lookup

https://rest.ensembl.org/documentation/info/lookup

https://rest.ensembl.org/documentation/