Question: Is there any way to convert ENST to HGNC symbol?
0
gravatar for Xiaohan Pan
2.5 years ago by
Xiaohan Pan10
Xiaohan Pan10 wrote:

I posted a question yesterday about how to get up and downstream genes name of my siggene from cuffdiff, details → enter link description here

I followed advice and BEDops was work, but what I got is a list of ENST, like this (NR4A1|CDS:ENST00000243050.5;CDS:ENST00000293662.8;CDS:ENST00000360284.7;CDS:ENST00000394824.2;CDS:ENST00000394825.5;CDS:ENST00000545748.5;CDS:ENST00000546756.1;CDS:ENST00000546842.5;CDS:ENST00000548232.1;CDS:ENST00000548977.5;CDS:ENST00000550082.5;CDS:ENST00000550582.2;CDS:ENST00000550763.1;CDS:ENST00000552049.5;CDS:ENST00000553200.1;CDS:ENST00000562373.1;ENSG00000123358.19;ENSG00000123395.14;ENSG00000161835.10;ENSG00000259884.1;ENST00000243050.5;ENST00000293662.8;ENST00000360284.7;ENST00000394824.2;ENST00000394825.5;ENST000)
I want to know is there any way to convert ENST symbol to HGNC symbol in a huge number? Maybe rely on some R packages or Python packages?

Your suggestion will be appreciated!

rna-seq gene • 2.0k views
ADD COMMENTlink modified 8 months ago by Xali Xraza0 • written 2.5 years ago by Xiaohan Pan10
1

try EnsDb.Hsapiens.v86 in bioconductor packages

ADD REPLYlink written 2.5 years ago by cpad011212k

Thank you very much!

ADD REPLYlink written 2.5 years ago by Xiaohan Pan10

You should try bioMart package at R.

ADD REPLYlink written 8 months ago by esraesmeray199010

best choice is to try EnsDb.Hsapiens.v86 in bioconductor packages

ADD REPLYlink written 8 months ago by Xali Xraza0
7
gravatar for Jean-Karim Heriche
2.5 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

Use EnsEMBL's BioMart or EnsEMBL's API. If you want to use R, there's the biomaRt Bioconductor package.

ADD COMMENTlink written 2.5 years ago by Jean-Karim Heriche21k
5
gravatar for genomax
2.5 years ago by
genomax76k
United States
genomax76k wrote:

Have you looked at BioMart at Ensembl?

ADD COMMENTlink written 2.5 years ago by genomax76k

I'll try, thanks so much

ADD REPLYlink written 2.5 years ago by Xiaohan Pan10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 768 users visited in the last hour