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 | 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 [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 |