Question: Make List Of All Human Gene Ids (Ens, Hgnc, Entrez) To Ease Conversion Of Ids
4
gravatar for ismeet.kaur
7.1 years ago by
ismeet.kaur40
India
ismeet.kaur40 wrote:

Is there any way to get all the human genes with their ENSG ID, ENSP ID, HGNC ID, and Entrez ID. Because while doing ID conversion I always fail to convert some of the IDs, either one or the other counterpart is missing, for which I have to manually search the database. Is there a way to make a comprehensive list of these genes with all these IDs in humans??????

ADD COMMENTlink modified 7.1 years ago by Ian5.6k • written 7.1 years ago by ismeet.kaur40
1

What is the 2015 way of doing this? Thanks.

ADD REPLYlink written 4.2 years ago by Tommy Carstensen190
1

Have you posted your code somewhere????

ADD REPLYlink written 3.3 years ago by Jack120
1
gravatar for Assa Yeroslaviz
7.1 years ago by
Assa Yeroslaviz1.2k
Munich
Assa Yeroslaviz1.2k wrote:

did you try biomaRt?

I think it is also possible with eutils, though I didn't try it.

ADD COMMENTlink written 7.1 years ago by Assa Yeroslaviz1.2k

@Frymor I used biomart but when I try to map some IDs the information seems to be missing which means its not complete reference to human genes. How can I solve it?

ADD REPLYlink written 7.1 years ago by ismeet.kaur40

do you have an example of what you did?

ADD REPLYlink written 7.1 years ago by Assa Yeroslaviz1.2k

BioMart is not working. It doesn't return any results.

ADD REPLYlink written 4.2 years ago by Tommy Carstensen190
0
gravatar for Irsan
7.1 years ago by
Irsan7.0k
Amsterdam
Irsan7.0k wrote:

Have a look at the international protein index (IPI) from EBI. They have prepared plain text files with gene cross references to many resources. For some reason the link to the ftp site seems to be broken but as soon as you find the right one you may find the file you are looking for

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by Irsan7.0k

IPI link is dead.

ADD REPLYlink written 4.2 years ago by Tommy Carstensen190
0
gravatar for Ian
7.1 years ago by
Ian5.6k
University of Manchester, UK
Ian5.6k wrote:

This Biostars link should be useful: Gene Id Conversion Tool

ADD COMMENTlink written 7.1 years ago by Ian5.6k
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