Enrichment Analysis in DAVID

Question

[ek699]

Hi, I have been working on the enrichment analysis on mouse RNA-seq data (mm10) I have been trying to upload my expressed gene file (about 15,000 rows are included. 120KB) as background, but unfortunately, I am unable to upload it on DAVID, since the website doesn't respond.

I have two files: up-regulated gene list and down-regulated gene list for the enrichment analysis and I want to create functional annotation chart per file.

Do you know how to upload my background file on DAVID successfully? Does an uploading error happens a lot in DAVID? I am also looking for any other tools for enrichment analysis, what would you recommend?

I looked at "Enrichr," but it seems like I cannot upload my own background file on the website. But, I need to upload a customized background file, so please let me know if there is any tool that I can use my background file like in DAVID.

I am new to bioinformatics, so any type of assistance is greatly appreciated. Thank you.

Answer 1

[colin.kern]

I have always just used the default background for the species. DAVID can be slow and unstable so I'm not surprised you're having trouble uploading a list of 15000. On a different note, I would reconsider whether it makes sense to do a GO term analysis separately on up-regulated and down-regulated genes. What is the interpretation you will make from those results? If you're intending to say that the functions enriched in the up-regulated genes are increased or enhanced and the functions enriched by the down-regulated genes are decreased, that's not a correct interpretation. A gene can be a negative regulator for another gene, so the down-regulation of gene A may cause an up-regulation of gene B, which in turn increases some function. Both gene A and gene B will be annotated with that GO term. If you want to determine if biological pathways are actually activated or suppressed by DEGs, rather than just enriched by them, I'm not sure you can do that in DAVID. I have used Ingenuity Pathway Analysis (IPA) to do this, but it's not a free tool. I'm sure there are free tools available that do similar things.