Ranking gene list for GOrilla gene ontology enrichment analysis
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?
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