I know there are existing GO slims predefined. But does anyone know how I can create my own collection of GO terms for enrichment analysis?
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$\begingroup$ I have never created one, but a GO slims is just a list of GO associated with genes, so you just need to download the list of GO and associate them with your list of genes. What have you tried/searched? What do you need that it is not covered in the FAQ? $\endgroup$– llrsNov 29, 2017 at 8:04
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$\begingroup$ GO slims are just a subset of the gene ontology graph. Just a group of terms, no genes. We can't help you create one if you don't explain what terms you want and what sort of analysis you want to do. $\endgroup$– terdon ♦Nov 29, 2017 at 8:33
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$\begingroup$ I have a list of genes enriched in kidney. So I want to get a list of kidney-related terms and see which of them are significantly enriched. $\endgroup$– Code42Dec 3, 2017 at 8:34
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$\begingroup$ @Dr_Hope Then what you really want is to test an enrichment in GO related to kidney not create a GO slim. But if you only use a subset of genes and a subset of GOs the test would be biased (AFAIk) if you don't tell the suitable background population of genes and GO terms. $\endgroup$– llrsDec 5, 2017 at 9:17
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$\begingroup$ I've already done a canonical GO to check the background. The enriched terms are mostly kidney-related because our sample is a kidney. That's why I need a GO slim to check kidney-only terms. $\endgroup$– Code42Dec 12, 2017 at 17:27
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