Different significance with ORA and GSEA

[Cristian Fiorucci]

Hello there,

I'm kinda knew to WebGestalt and enrichment analyses in general and i'm trying to analyze a recent RNAseq data. 
After many try, i analyzed up and down regulated genes in my list but i found some differences.
When i ran UP or DOWN regulated genes with ORA method i found some Biological Process for each enrichment, but when i ran up and down genes (together with Log2FC) with GSEA it clusterized only upregulated genes, 'cause for the program downregulated have >0.05 FDR. Is it normal, or i have to change some settings?

Examples are attached, obviously genes are from the same list but in ORA i have uploaded up and down separately while in GSEA all at once with Log2FC

Can you help me?

[Yuxing Liao]

Hi Cristian,

I would say it is pretty normal. ORA is much simpler and depends on many things such as how you threshold your data.

Yuxing

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[Cristian Fiorucci]

Thank you for your help!