Question: How To Search Disease Association For A List Of Genes?
6
gravatar for k810v9
5.8 years ago by
k810v960
k810v960 wrote:

Hello,

This is my first post in your website. I would like some help regarding the following issue:

I have a list of 130 genes and I would like to perform a batch web search to see if any of them is associated with a specific trait (e.g. "psoriasic arthritis" or "annular pancreas" or "single ventricle"). The search term would be something rather specific.

Do you know of any web tool to paste my gene list and provide me results or scores for each of the genes?

Thank you in advance,

Konstantinos

gene search list disease • 7.9k views
ADD COMMENTlink modified 4.1 years ago by TriS3.6k • written 5.8 years ago by k810v960
5
gravatar for Tky
5.8 years ago by
Tky990
Japan
Tky990 wrote:

Genotator database from the Wall lab is a nice resource to get all genes related with a given disease/disorder. check http://genotator.hms.harvard.edu/geno/disorders/

ADD COMMENTlink written 5.8 years ago by Tky990

Just saw Genotator. It looks very good. It says it uses OMIM, GeneCards, HuGENavigator, GenAtlas, YFG, PharmGKB, EXPASY, WikiGenes, Entrez, and GAD. I did notice some genes missing from it for some disorders, but it seems by and large a good choice. It also does not seem to have the GWAS Catalog results in there though I think a few of the databases above would include things found by GWAS.

ADD REPLYlink written 5.8 years ago by Ryan D3.3k
4
gravatar for Giovanni M Dall'Olio
5.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

The database for Gene Associations with disease is OMIM.

To make a batch search in OMIM, you have two options: either use the OMIM APIs, or alternative use Biomart.

If you search for "gene association enrichment" in biostar you will find many similar discussions.

ADD COMMENTlink written 5.8 years ago by Giovanni M Dall'Olio26k
2
gravatar for Dataminer
5.8 years ago by
Dataminer2.6k
Netherlands
Dataminer2.6k wrote:

Hi!

May be FunDo is useful for you, have look at this link http://django.nubic.northwestern.edu/fundo/faq

and don't forget to accept or upvote the answers which were helpful to you ;)

have fun

ADD COMMENTlink written 5.8 years ago by Dataminer2.6k
1
gravatar for ancient_learner
5.8 years ago by
India
ancient_learner610 wrote:

You can try Genecards or GeneAlacart for this. especially GeneAlacart, you can register for free and get the all available information for the set of (200) genes at a time. it retrieves data from OMIM as well as other databases to see their role in various diseases.

ADD COMMENTlink written 5.8 years ago by ancient_learner610
1
gravatar for TriS
4.1 years ago by
TriS3.6k
United States, Buffalo
TriS3.6k wrote:

maybe a lil late, but DisGeNET also provides association between genes and disease.

ADD COMMENTlink written 4.1 years ago by TriS3.6k
0
gravatar for k810v9
5.8 years ago by
k810v960
k810v960 wrote:

Thank you all for your answers. Actually I am a clinician with very little knowledge in bioinformatics.

Of course I am aware of OMIM. However, I would like to do the opposite thing. Instead of searching the database for "Annular pancreas" and get the respective 'gene map' (the simpliest way to have the genes in a "table" I would like to see if each of the genes in my list has the term "annular pancreas" in the respective omim entry.

A good alternative would be to retrieve only the list of genes from the 'gene map'. Unfortunately I cannot copy only this column of the table. Any ideas?

Genotator seems to be interesting. Is there a clear (1:1) association between the genes and the phenotype or does it also have data from GWAs, etc?

GeneAlacart is indeed very good, I just tried it following anurupadevi 's suggestion.

Any other ideas?

ADD COMMENTlink written 5.8 years ago by k810v960
1

Please post responses and further questions as comments under the answers, rather than posting them as a new answer.

ADD REPLYlink written 5.8 years ago by Neilfws48k
0
gravatar for bioinformationcn
5.8 years ago by
bioinformationcn0 wrote:

I have build a database of gene to disease, the original data is form COSMIC (http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/), if you are interest it, I can send to you.

ADD COMMENTlink written 5.8 years ago by bioinformationcn0
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