Get The List Of Genes Associated With A Disease

Question

[toshnam]

Hi all,

I want to find certain disease-associated genes among Mendelian disease (such as Alzheimer and Schizophrenia disease), and then I'll study about the correlation of them.

I searched for OMIM using Alzheimer disease, and I got 298 search results containing various Alzheimer disease (AD) types. I don't know which one should I choose in various disease type. Also, APOE gene is known as a gene that plays an important role in AD, but some disease types are not related with APOE gene in OMIM.

I want to get the known certain disease-associated gene list. Please help me for it.

[Giovanni M Dall'Olio]

I have changed the title to make it clearer, please check it

[Giovanni M Dall'Olio]

what could be the most appropriate title for this question? "Get the list of genes associated with a disease?"

Answer 1

[Lars Juhl Jensen]

If you want the most comprehensive list of genes associated with Alzheimer's Disease, I think you would be best off not using OMIM. Instead, I would go to Alzforum, where specialists on the disease maintain a directory of genes with a role in Alzheimer's disease. Similarly, I would take a look at the SZGene database, which is a resource of genes involved in Schizophrenia.

I think that this is a general trend - if you want the best possible list of genes believed to be involved in a well-known disease, you are usually best off using out the specific database maintained by the community of researchers working on the disease in question.

Answer 2

[Khader Shameer]

I am working on comorbidity analysis of various diseases and find the Disease Ontology (DO) and Disease Ontology - Lite (DO-Lite) based annotations very efficient in mapping a given gene to different diseases.

For example:

• List of genes associated with Alzheimer's Disease from DO-Lite mapping
• List of genes associated with Schizophrenia using DO-Lite mapping

You can also check the FunDo webserver which can map a bunch of genes to DO-Lite. Also there is an R package (GeneAnswers) and .db (DO.db) for disease ontology analysis.

Answer 3

[Larry_Parnell]

I would look through the 7999 gene-disease associations from Zhang, Becker et al. This is an excellent set that comes from curation of data on disease phenotypes from both human and mouse. They identified 115 Alzheimer genes, from A2M to WT1.

What I also like about this gene set is the hierarchical nature of organizing the diseases. There are 23 disease classes - Nervous systems diseases, or Neoplasms, for example. Each of these classes is then a parent to numerous child terms, 480 in total. As the research group is based at NIA, the diseases have a focus toward aging and are indeed relevant to most research groups.

Answer 4

[zx8754]

Genotator: A disease-agnostic tool for genetic annotation of disease

http://genotator.hms.harvard.edu/geno/disorder/alzheimer_disease/