Background genes for enrichment analysis

When computing GO categories enrichment it makes sense to narrow down the list of genes the signature is analyzed against (see computation footnote to see how background is used). GOnet allows to use three types of background option:

Computing GO enrichment p-values

Computation of enrichment p-values follows the procedure in Python goenrich package. For every GO term considered, the p-value in Fisher exact test is computed. For every term null hypothesis states that the number of genes in the input list annotated with the GO term is not overrepresented compared to the background. The contingency table considered is:

Entries in background and in input listEntries in background but not in input listTotal
Annotated with GO termxn-xn
Not annotated with GO termN-xM-N-(n-x)M-n

A p-value is computed as a survival function of hypergeometric distribution with shape parameters (M, n, N) at point x.