PRSet: Question about Which Gene Set to Choose

[jueqiw]

Hi Dr Shing Wan Choi,

Thanks a lot for your interesting work! I am trying to run the PRSet on my target datasets about Alzheimer's disease and ASD. But I wonder, do you have any recommendations on which gene set I should choose from? Is it possible for you to share the MSigDB files and gene gtf files of the schizophrenia task with me?

Thanks in advance.

Jueqi

[choishingwan]

It’s an important research question and there really isn't a one size fit all solution I’d recommend you to try and run MAGMA on the summary statistics on the msigdb sets Sam

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On Wed, Nov 13, 2024 at 7:36 PM Jueqi Wang ***@***.***> wrote: Hi Dr Shing Wan Choi, Thanks a lot for your interesting work! I am trying to run the PRSet on my target datasets about Alzheimer's disease and ASD. But I wonder, do you have any recommendations on which gene set I should choose from? Is it possible for you to share the MSigDB files and gene gtf files of the schizophrenia task with me? Thanks in advance. Jueqi — Reply to this email directly, view it on GitHub <#371>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYTIVXB66NGHKN5KXQD2APWCHAVCNFSM6AAAAABRXWXD5WVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY2TOMJZGYYDQNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jueqiw]

Hi, Dr Shing Wan Choi,

Thanks a lot for your reply. I just finished running MAGMA on the summary statistics data I have. I tried to run MAGMA on msigdb sets of Canonical pathways, Ontology gene sets, and hallmark gene sets. I discovered that Ontology gene sets should suit my tasks better (give me more gene sets with p-values less than 0.05).

Can I ask for a recommendation for the next step, such as whether I would run the Ontology gene sets (which contain 16107 gene sets) with PRSets?

Thanks,

Jueqi