what the best gene set enrichment analysis online tool for computing enrichement p-values ?
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Entering edit mode
8.2 years ago
jack ▴ 960

Hi all,

I have ranked list of small RNA interactions called A. also I have other set small RNAs interactions called B.

I want to see that, whether the set B enriched in top or down of ranked list A? So I need to have plot based on P-value. because these interactions are not genes and does not have standard IDs which most of the gene set enrichment analysis tool need, I can not use them. Does someone knows how can I compute it ?

Here is an example of my dataset :

Ranked list A:

"CENPT-MIMAT0000077"   "WDR43-MIMAT0000068"   "P4HA2-MIMAT0000082"  "NONO-MIMAT0000086"    "CNOT2-MIMAT0000086"   "CREB3L1-MIMAT0000081" "PLA2G6-MIMAT0000077"  "LIG1-MIMAT0000077"    "IFT46-MIMAT0000076"


set B :

CREB3L1-MIMAT0000081" "PLA2G6-MIMAT0000077"  "LIG1-MIMAT0000077"


I need the result as plot with p-values

genome RNA-Seq R • 2.5k views
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8.2 years ago
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Entering edit mode

the problem is that, I have one ranked list, without any class information. I want to compute the enrichment of B in ranked list A. but the one you suggested, it need more inputes