Dear all,
I have a list of about 800 genes and I would like to annotate associated disorders/diseases. If possible, I would like to add some disease groups as well (e.g. if the disorder is an inherited metabolic disease or a neuromuscular disease and so on...).
Does anyone know where I could find this information? I tried OMIM - however, their data is not easily accessible...
Thanks!
Heiko Brennenstuhl There are several online servers and applications that you can try. I would recommend starting with DiGeNET. You can plug-in your list of genes. Once, you get the results, you can click on the summary of gene-disease associations and it will give you all the details including classes/groups of diseases. You just need to do some processing of your 800 genes before submitting. They need to be each separated by :: I do not know if it supports uploading 800 genes but you can give it a try.
https://www.disgenet.org/search
You can also try other enrichment tools which compile disease gene data from multiple resources, including OMIM. Here are some of those:
ToppGene Suite (ToppFun Application): This is developed by us.
EnrichR
Metascape
Hope that helps
Bes
Anil
Orphanet is great but includes rare diseases only. Plus, it does not provide any interface wherein you can submit a list of genes and find out what diseases are associated with them. The only way you can do that is to download their data files and then use that for comparing your gene set.
BTW, I forgot to mention that data in DisGeNET could be stale. I do not think the data is up-to-date. There have been no new versions since 2020.
Have you tried CTD database? You can use SetAnalyzer tool to extract diseases from the input gene list (https://ctdbase.org/tools/analyzer.go)
CTD is great but just be careful that majority of the disease-gene associations in there are inferred associations captured via a chemical interaction.
Set analyzer is not an ideal option for this type of query. You can instead try their batch query and select "Curated" for disease associations.
https://ctdbase.org/tools/batchQuery.go
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