GOEnrichment is a Java application that can be used to analyze gene product sets (e.g., from microarray or RNAseq experiments) for enriched GO terms.
GOEnrichment requires:
GOEnrichment produces a tabular result file and a graph file for each GO type (MF - Molecular Function, BP - Biological Process and CC - Cellular Component):
The graph is colored by p-value: terms with p-value above cut-off appear in white; and the color gets darker as the p-value decreases
(see the scale at https://github.com/DanFaria/GOEnrichment/blob/master/Scale.png). In addition to the name of each GO term, the graph shows its frequency in the study set. Dashed edges indicate that one or more intermediate terms were ommited from the graph.
Gene products listed in either the study or population set files that are not present in the annotation file will be ignored.