How to get all disease-causing genes from OMIM?
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7.2 years ago
naulty ▴ 10

Hello,

I've watched a video from YouTube about OMIM. Then I get that OMIM already had more than 3000 disease-associated genes till last year. Now I want to get all of those genes from OMIM to do some experiments. 

I think maybe I should use "Gene Map" of OMIM, but  I still don't know how to search to get all disease-associated genes.

Do you have any good advice or guide?

Thank you in advance,

naulty

OMIM disease gene • 12k views
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7.2 years ago

First of all, let's clarify that in OMIM there are two types of IDs:

- the MIM Gene ID refers to genes (.e.g 600276)

- the MIM MORBID ID refers to diseases/phenotypes ( e.g. 125310)

It is easy to make confusion, because both types of IDs are integer and there is no easy way to tell whether an ID refers to a gene or to a disease. If you look for example at the MORBID ID www.omim.org/entry/125310, you will see that it is associated to at least one gene.

To download all the genes, you can use the page posted by Santhilal Subhash, parsing the files morbidmap and genemap in order to get the ids. An alternative is to download them from Biomart, selecting no filters, and the MIM Ids in the Output tab. This will give you a list of all the genes and their association to disease, with the advantage that you can select other output columns to get other information about the genes.

 

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Thank you very much.

I've tried the method you and Denise told me. But I'm not quite sure which Datebase and Dateset I should choose. I've tried several times and the number of entries I got everytime is more than 15000.

And I want to stress that I just want to get the genes with disease-causing, not all genes have MIM IDs. I checked out the "OMIM Gene Map Statistics" on omim.org, I think maybe all I want are the "3298 genes with phenotype-causing mutation" said on the website. But I still don't know how to do.

Maybe I undetstand the method you said in a wrong way, I hope you can give me some advice.

Thank you!

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Sorry, maybe I'm wrong, maybe the disease-causing genes are not equal to the genes with phenotype-causing mutation.

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I find that maybe I just need to download the "morbidmap" from OMIM to get all the disesase genes.
 

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7.2 years ago
EagleEye 7.2k

You can download MIM ids and corresponding GeneID from here:

http://www.omim.org/downloads

 

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7.2 years ago
Denise CS ★ 5.2k

I endorse the alternative BioMart. I'd perhaps point to another link as well. The reason for that is due to the fact that there can be a lag between the latest version of the Ensembl database from our main site (as part of our release cycle) and the version available in Central BioMart. At the moment they are in sync but as soon we release a new version, it takes some time for them to update it. So just keep an eye on that...

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I now have the same question but need to compare with Orphanet  so the above comments are useful thanks.  OMIM just explained on Twitter that their servers are download capped so I cant drop query lists out :( (yes maybe I'll sign up for API sometime).   However, in the meantine  I get differences in numbers.

From  http://omim.org/statistics/geneMap "genes phenotype-causing mut" = 3,416.

But "phenotype description, molecular basis known" =  4,482  then select "Gene Map" = 3,554

BioMart Ensembl Genes with Swiss Prot IDs and MIM phenotype  =  3268

OK these are small differences but if the OMIM and/or Biomart folks have an explanation that would be useful

 

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