Question: what the best gene set enrichment analysis online tool for computing enrichement p-values ?
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gravatar for jack
4.3 years ago by
jack750
Germany
jack750 wrote:

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 .

bioinformatics rna-seq R genome • 1.5k views
ADD COMMENTlink modified 4.3 years ago by Alex Reynolds28k • written 4.3 years ago by jack750
1
gravatar for Alex Reynolds
4.3 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

http://systems.crump.ucla.edu/rankrank/rankranksimple.php might help.

ADD COMMENTlink written 4.3 years ago by Alex Reynolds28k

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

ADD REPLYlink written 4.3 years ago by jack750
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