Ranking gene list for GOrilla gene ontology enrichment analysis

Question

[Mikael]

Hi,

I did a differential expression analysis using RNA-seq data from control and gene knockdown cells. Now I have a DE gene list and I want to do a gene ontology enrichment analysis using GOrilla, but I am not sure how to rank the gene list.

Should I rank the genes based on adjusted p-value, log2fc or some other metric? Also, should I perform separate analyses for up- and downregulated genes?

Cheers!

[Hyper_Odin]

Generally, I filter the genes that pass the adjusted p-value of < 0.05, and then separate the list in to 2 groups based on log2fold change.

1. Upregulated (>0.585)
2. Downregulated (<-0.585)

(<-0.585 and >0.585 converts to -1.5 and 1.5 in FC).