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Question: GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogenic Signatures or GO IDs using rGREAT
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Hi All, I used rGREAT to do GO enrichment analysis for the peak calls from macs2, where I got enriched GO IDs and MSigDB Oncogenic Signatures. Can anyone help me to automate this process in such a way that I will get a table with all enriched GO IDs or MSigDB Oncogenic Signatures with corresponding significant genes? Thank you

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What have you tried? What final output do you want? We need hard examples of what you have, what you've tried, and what you expect to get out at the end. We can't help you much otherwise.

ADD REPLYlink 8 months ago
jared.andrews07
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Hi @jared

I have a list of annotated chip-seq peaks and their corresponding genes. In order to check if there is any enrichment for the genes that are from any specific oncogenic or any immunological pathway, I have used rGREAT. rGREAT with its getEnrichmentTables() provided me a file with list of enriched pathways and their significance level. But it doesn't tell which genes were used and overlapped with a pathway of my interest.

Can you suggest any smart approach to do the same?

I hope it is clear and make sense now.

ADD REPLYlink 8 months ago
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