Make List Of All Human Gene Ids (Ens, Hgnc, Entrez) To Ease Conversion Of Ids

Question: Make List Of All Human Gene Ids (Ens, Hgnc, Entrez) To Ease Conversion Of Ids

6.4 years ago by

India

ismeet.kaur • 30 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??????

gene database snp biomart conversion • 6.7k views

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modified 6.4 years ago by Ian ♦ 5.4k • written 6.4 years ago by ismeet.kaur • 30

What is the 2015 way of doing this? Thanks.

ADD REPLY • link written 3.5 years ago by Tommy Carstensen • 150

Have you posted your code somewhere????

ADD REPLY • link written 2.6 years ago by Jack • 80

6.4 years ago by

Assa Yeroslaviz • 1.2k

Munich

Assa Yeroslaviz • 1.2k wrote:

did you try biomaRt?

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

ADD COMMENT • link written 6.4 years ago by Assa Yeroslaviz • 1.2k

@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 REPLY • link written 6.4 years ago by ismeet.kaur • 30

do you have an example of what you did?

ADD REPLY • link written 6.4 years ago by Assa Yeroslaviz • 1.2k

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

ADD REPLY • link written 3.5 years ago by Tommy Carstensen • 150

6.4 years ago by

Irsan • 6.8k

Amsterdam

Irsan • 6.8k 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 COMMENT • link modified 6.4 years ago • written 6.4 years ago by Irsan • 6.8k

IPI link is dead.

ADD REPLY • link written 3.5 years ago by Tommy Carstensen • 150

6.4 years ago by

Ian ♦ 5.4k

University of Manchester, UK

Ian ♦ 5.4k wrote:

This Biostars link should be useful: Gene Id Conversion Tool

ADD COMMENT • link written 6.4 years ago by Ian ♦ 5.4k

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