Obtaining gene specific annotations for mouse genes
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3 months ago
Stevens • 0

Hi, I have KO and WT cells that have been pre-analyzed and I am attempting to use the R package iDEA to identify biological pathways involved in the behaviour of my KO cells.

iDEA requires a gene specific annotation file that has matching gene names to the DE file created during pre-analysis, however I am finding it difficult to find a gene specific annotation file that works with my data or that is specific to mice

I have found a couple of resources but I am not sure how to utilize them either.

Any information about possible gene specific annotation files is appreciated.

mouse enrichment set iDEA gene • 290 views
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Looking at the iDEA manual, they do provide a link to download pre-formatted mouse gene set annotation files (at least for GOs).

I see that those files contain genes with the MGI ID nomenclature. If your DE file contains genes with a different nomenclature, you could use the R package biomaRt to convert them to MGI IDs.

If you want a database with many gene set files from the MsigDB (GO, KEGG, Reactome...), you could try the R package msigdbr. The gene sets are annotated with entrezgen ID, ensembl ID and gene symbol. But you would have to format its files into the format used by iDEA.

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Thanks, I have tried out the dataset within R, its names aren't overly informative so I'm also testing out a dataset from msigdb. The result from idea's mouse gene set didn't return any pathways at a significant level so I'm trying to work out if something's wrong with my data or the gene set now. Alot of my p-values in the DE were 0 from being too low so that may be the problem.

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OK, there is always the case that there are in fact no enriched pathways. Aside from the programmatic approach, you can get a quick overlook of which pathways you would expect to be enriched if you submit your list of significant genes to the Enrichr web (it looks across many many databases).

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I've considered that, but there were alot of differentially expressed genes so even by chance theres likely to be a few pathways. I'm not entirely sure how to navigate enrichr but it gave alot of results so it may be something wrong with my input data in iDEA

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