How to validate the association between a ranked list of genes found computationally and a disease?

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4.9 years ago

Davide Chicco ▴ 120

Hi all

I applied some bioinformatics methods to retrieve the genes related to a cohort of patients having a particular disease and to a cohort of healthy controls.

I then applied some biostatistics and machine learning techniques to rank all the genes based on their importance/significance in relation to the disease. Now I have this ranked list of genes and my next step is to try to validate it.

What's a precise computational way to find confirmation (or disproval) of the association between the top genes of my ranking and the studied disease?

How can I demonstrate that the genes A, B, C are related to the studied disease D?

Thanks!

-- Davide

gene diseases validation • 867 views

ADD COMMENT • link 4.9 years ago by Davide Chicco ▴ 120

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If you have list of genes associated with disease, you could do GSEA.

ADD REPLY • link 4.9 years ago by GouthamAtla 12k

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As mentioned, GSEA is a good bet. Could also try something like DOSE.

ADD REPLY • link 4.9 years ago by jared.andrews07 ★ 16k

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