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What is Gene set enrichment?

Enrichment analysis is a technique commonly used to add biological context to a list of genes, such as list of significant genes. The procedure is based on assigning genes to groups and then finding overrepresented groups in filtered gene lists using a Fisher's exact test.

Running Gene set enrichment

We recommend filtering to a set of genes you want to test for enrichment, but Gene set enrichment will run on any Feature list data node. 

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The result is stored under an Enrichment task node. To open it, double click on the node or select the respective Task report from the context sensitive menu.

Gene set enrichment task report

Figure 4 shows an example Gene set enrichment task report. The table contains one gene set per row (Gene set column; the column entries are hyperlinks when using the distributed GO gene sets), with the category name in the Description column. The categories are ranked by the Enrichment score, which is the negative natural logarithm of the enrichment p-value (P-value column) derived from Fisher's exact test on the underlying contingency table. The higher the enrichment score, the more overrepresented the GO category is within the input list of significant genes. The columns can be searched by typing in the search term in the respective box (and hitting Enter), or sorted by selecting the double arrow icon ( ).

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References

1. Ashburner M, Ball CA, Blake JA et al. Gene Ontology: tool for the unification of biology. Nat Genetics. 2000; 25:25-29.
2. The Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015; 43:D1049-1056.Recommended citations from the Geneontology.org website

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