Enrichment Test

This tool is to test the enrichment of a sub-network in a biological pathway. Sub-network and pathway is given in gene set file format. Hypergeometric probability between two gene sets is estimated.
Source \ Target True False total
True k m - k m
False n - k N + k - n - m N - m
total n N - n N

hypergeom.gif

Input

Usage : enrichment [OPTION]
Options:
    -s           source gmt file
    -t           target gmt file
    -p           p-value cutoff
Example: enrichment -s test.gmt -t HumanGO_biological_process.gmt -p 0.001

Sample pathway and GO gene set files.
HumanGO_biological_process.gmt
HumanGO_cellular_component.gmt
HumanGO_molecular_function.gmt
ReactomePathways.gmt

Output

ID, description and p-value.
Amine Oxidase reactions	Reactome Pathway	0.000995966039629708
Dopamine clearance from the synaptic cleft	Reactome Pathway	0.000747123462978736
Enzymatic degradation of Dopamine by monoamine oxidase	Reactome Pathway	0.00049818161228934
Enzymatic degradation of dopamine by COMT	Reactome Pathway	0.00049818161228934
Metabolism of serotonin	Reactome Pathway	0.00049818161228934
...

  • For FDR estimation, you can use GSEA or GSA.

Last edited Feb 13, 2013 at 2:43 PM by yongkeecho, version 5

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