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).
AlzPathway, if you have not seen it.
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.
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.
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 ;-)
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