Table 1.

Description of functionalities supported by different tools focused on biological interpretation from GO annotation

Tool	Interface, Langage	GO Annotation Database	Input identifiers for GO annotation	Enrichment test	GO terms SS	Sets of GO terms SS	Visualization	Multiple lists	Graph interactivity
David https://david.ncifcrf.gov/ [11, 12]	Web	Fixed release, Ensembl, Entrez, Uniprot	GeneID, Ensembl gene ID, Affymetrix probes, Illumina ID, Agilent ID (Do not allow lists of > 3000 identifiers)	Fisher Exact (EASE)	No (used gene’s Kappa similarity)	No	summary table, bar plot, Gene-term 2D view, clustering (centered genes)	Yes	No
ClusterProfiler Bioconductor [13]	R	Current release, Bioconductor databases	GeneID, Ensembl gene ID, can be converted in the module	Hypergeometric	IC-based, Graph-based (computed)	Yes	summary table, bar plot, dot plot, enrichment map, network	Yes	No
gProfiler https://biit.cs.ut.ee/gprofiler/ [14]	R, Web	Fixed release, Ensembl supported species	mixed types of gene identifiers converted to Ensembl gene ID	Hypergeometric	No	No	tree like list of enriched GO terms, summary table	Yes	No
REVIGO http://revigo.irb.hr/ [15]	Web	Fixed release, UniProt and supported several species	No	No	IC-based (computed for visualization)	No	summary table, scatter plot, interactive map, TreeMap, export R plot (centered GO terms)	No	Yes
ViSEAGO Bioconductor	R	Old and current release, Ensembl, Entrez, Uniprot, Bioconductor databases	GeneID, Ensembl gene ID, Uniprot ACC	Fisher Exact	IC-based, Graph-based (computed for visualization)	Yes	summary table, bar plot, upset, MDS plot, clustering (centered GO terms)	Yes	Yes