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Table 1 Description of functionalities supported by different tools focused on biological interpretation from GO annotation

From: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

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
[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
R Current release, Bioconductor databases GeneID, Ensembl gene ID, can be converted in the module Hypergeometric IC-based, Graph-based
Yes summary table, bar plot, dot plot, enrichment map, network Yes No
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
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
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