GO term Enrichment vs Annotation analysis

GOnet supports two types of analysis available under Analysis type field in the submission form. They differ in which subset of Gene Ontology the query should be analyzed against.

1. GO terms statistically significantly over-represented in the gene list submitted.
2. A predefined subset (also known as “GO slim"), or a user-supplied list of terms.

In the first case the analysis will be termed to as an “enrichment” analysis, in the second as an “annotation” analysis. The first one (default) runs standard GO enrichment analysis and shows relation of the submitted genes only to over-represented GO terms. In the second case GOnet will reconstruct relationship of the input genes to GO terms specified in GO subset parameter. For example, “GO slim generic” can be selected. This is a subset of Gene Ontology maintained by GOC which includes categories suitable for majority of studies. Alternatively one can select custom option and specify GO terms in appearing text field.