How to extract the reference gene sets of the diseases in DisGeNET?

[levinhein]

How to extract the reference gene sets of the diseases in DisGeNET?

[dhimmel]

What do you mean by the "reference gene sets"? Can you point to where these gene sets are documented?

Note this is not the official DisGeNET repository, so please update this issue with the solution you discover, but unlikely we will be able to help much.

[levinhein]

Hi. Thanks for your reply.

DisgeNET allows prediction of diseases associated with an input list of genes. For example, if I input N genes, the output basically gives summary information about diseases associated with a smaller subset of the input N genes.

Here's an example DisGeNET output using Enrichr online tool.

These diseases in the barplot represent n genes from the total input gene list that are associated with it. For example, if the input was 100 genes, and in this result "Liver Failure" has 50 genes associated with it, then how can I get all the genes in DisGeNET that are associated with "Liver Failure" term.

As a comparison, like in gene set enrichment analysis (GSEA), if you have input 100 genes, result will show that 75/100 genes are related to pathway A. But, those pathways have a fixed/original total number of genes in KEGG/REACTOME/etc. In this case, for example, I'm interested in retrieving the complete list of genes in pathway A-KEGG.

[dhimmel]

Ah thanks @levinhein for that helpful explanation. Not something I can immediately help with but interested if you figure out how to access the gene sets.

[dhimmel]

how can I get all the genes in DisGeNET that are associated with "Liver Failure" term.

Isn't "Liver Failure" classified as a disease, so perhaps you just need to find all genes associated with Liver Failure based on some threshold? Perhaps it's the list shown at https://www.disgenet.org/browser/0/1/0/C0085605/?