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

Question

[ismeet.kaur]

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??????

[Tommy Carstensen]

What is the 2015 way of doing this? Thanks.

[Jack]

Have you posted your code somewhere????

Answer 1

[Assa Yeroslaviz]

did you try biomaRt?

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

[ismeet.kaur]

@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?

[Assa Yeroslaviz]

do you have an example of what you did?

[Tommy Carstensen]

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

Answer 2

[Irsan]

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

[Tommy Carstensen]

IPI link is dead.

Answer 3

[Ian]

This Biostars link should be useful: Gene Id Conversion Tool