Convert unigene ID to ensembl ID
3
2
Entering edit mode
4.2 years ago
jehu ▴ 30

Hi

Is there a way to convert UniGene ID to ensembl id? using python (my preference) or R?

some Unigene ID: Hs.509736 Hs.467701 Hs.138860 Hs.124611 Hs.460988 Hs.49787 Hs.412707 Hs.43697 Hs.447458 Hs.436618 Hs.465087 Hs.439552 Hs.183428 Hs.219140 Hs.153863 Hs.181163 Hs.499891 Hs.410037 Hs.519601 Hs.75640 Hs.450230 Hs.133892 Hs.450230 Hs.529609 Hs.16355 Hs.59332 Hs.501928 Hs.460095 Hs.23585 Hs.519469 Hs.363396 Hs.433732 Hs.82101 Hs.82101 Hs.79625 Hs.503001

Thank you so much!

mapping gene python R Ensembl • 3.2k views
ADD COMMENT
0
Entering edit mode

Hi, I have some problems with annotation among my dataset. I'm new in bioinformatics and I have Unigene ID (I believe) and I want to change it to ENSEMBLE ID, ENTREZ ID and most likely to GENE ID. For example my ID names, that I have in one column in my dataframe:

Hs00197954_m1 Hs01106910_g1 Hs01878570_s1

and I want gene symbols: MIA-RAB4B FGFR4 GPR160 I also can convert it into entrez ID or ensemble ID. I read that Unigene database is retired since 2019, and all functions from previous years don't support this database. How can I make this annotation happen in 2019 using R and RStudio?

Thank you for your help!

ADD REPLY
5
Entering edit mode
4.2 years ago
Spacebio ▴ 200

I used this script in python:

import mygene

mg = mygene.MyGeneInfo()

xli = open("LIST_OF_IDs_TO_CHANGE.txt")

out = mg.querymany(xli, scopes = 'unigene', fields = 'ensemblgene', species = 'human', returnall = True)
print out

I hope it helps!

ADD COMMENT
5
Entering edit mode
4.2 years ago
Spacebio ▴ 200

Same but R option:

library(mygene)

genes <- read.table("GeneName.txt", header = TRUE, sep = "\t")
y <- queryMany(genes, scopes = "unigene", fields = "ensemblgene", species = "human", returnall = TRUE)
ADD COMMENT
2
Entering edit mode
4.2 years ago

Have you tried BioMart? Also available in R.

ADD COMMENT
0
Entering edit mode

Am I doing something wrong or is the unigene not part of ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") anymore? Can't find it in the listAttributes().

ADD REPLY

Login before adding your answer.

Traffic: 1463 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6