Question: How to get a full list of biological pathways involved in Alzheimer's?
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gravatar for anne
2.1 years ago by
anne0
anne0 wrote:

Hi all, what is the easiest way to get a list of all known pathways involved in a disease? For example, I would like to have list of biological pathways known to be involved in Alzheimer's. I a next step, I would like to retrieve a list of genes known to be involved in those pathways (also happy to get hints for that).

search alzheimer's pathway • 936 views
ADD COMMENTlink modified 2.1 years ago by Denise - Open Targets4.9k • written 2.1 years ago by anne0
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gravatar for genomax
2.1 years ago by
genomax65k
United States
genomax65k wrote:

AlzPathway, if you have not seen it.

ADD COMMENTlink written 2.1 years ago by genomax65k
2
gravatar for Denise - Open Targets
2.1 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.9k wrote:

Have a look at the Open Targets Platform. We have 14 targets associated with Alzheimers disease based on information coming from Reactome (pathway R-HSA-8862803). The pathways we used in our analyses to associate a gene with a disease are all affected by pathogenic mutations. Those 14 targets are the genes you are looking for. Affected pathways are not the only piece of evidence we use. We have other data sources (genetic variants, drugs, RNA expression, Text mining and animal models). And for each of those genes, e.g. APP you can get a lot of information including Gene Ontology. The data from Open Targets is available programmatic access as well.

ADD COMMENTlink written 2.1 years ago by Denise - Open Targets4.9k
1
gravatar for Jean-Karim Heriche
2.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

KEGG has a disease database which represents each disease as a pathway, e.g. Alzheimer's. Reactome also has diseases annotations (not sure how to get them though). Another way would be to collect all the genes known to be involved (for example using DisGeNET) and aggregate their Gene Ontology annotations or pathway memberships from your favorite pathway database.

ADD COMMENTlink written 2.1 years ago by Jean-Karim Heriche18k
0
gravatar for Benn
2.1 years ago by
Benn6.6k
Netherlands
Benn6.6k wrote:

Easiest way is to search for "alzheimer" on websites, such as Reactome or GO. For example:

http://www.reactome.org/content/detail/R-HSA-8862803

http://amigo.geneontology.org/amigo/search/ontology?q=alzheimer

If you want to fetch the genes, you'll better get into R is my hint ;-)

ADD COMMENTlink written 2.1 years ago by Benn6.6k
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