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Table 1 Comparisons of MonaGO with existing GO analysis systems with visualisation capabilities

From: MonaGO: a novel gene ontology enrichment analysis visualisation system

System Interactive Visualisation of enriched GO terms Platform/dependency Download/save data Find similar terms/select important terms Show relationship between GO terms Flexible switching between pages Flexible threshold (p-value, etc.) Input list Examples
MonaGO Yes Chord diagram Browser Yes Yes Yes Yes Yes Genes, GO terms, previous visualisation Yes
agriGO [24] No Node-link diagram Browser Yes Yes Yes No (visualisation a subsequent step/page) Yes Genes, Probes Yes
AmiGO [25] No Node-link diagram Browser Yes Yes Yes No Yes Genes No
BiNGO [20] Yes Node-link diagram Cytoscape Yes Yes Yes Yes Yes Graph or gene list input Yes
DAVID [2] No Clustering, map Browser, programmatically (Java, Perl, Python) Yes Yes Yes No (several pages No Genes Yes
GOEAST [21] No Node-link diagram Browser Yes Yes Yes Yes Yes Probe set ID No
GOplot [19] No Circle plot, chord plot R Yes Yes Yes No Yes GO terms only Yes
Gorilla [17] No Node-link diagram with highlights Browser Yes No (abstract and redundant hierarchy) Yes No Yes Genes, proteins Yes
g:Profiler [16] No Bar chart, Word cloud Browser Yes Yes (by ranking) No (matrix denotes common genes between GO terms) No Yes Genes, proteins, probes Yes
Metascape [26] No Node-link diagram, Bar chart Browser, Cytoscape Yes Yes Yes Yes No RetSeq, Ensembl, Uniprot, UCSC Yes
PANTHER [3] Yes Pie chart Browser Yes Yes Yes No (several pages) No Genes, proteins Yes (only format, no complete examples)
REVIGO [10] Yes Node link diagram, Treemap Word cloud, Scatterplot Browser Yes Yes Yes Yes Yes GO terms Yes
WebGestalt [18] Yes Node link diagram Cytoscape Yes Yes Yes (but no interactive details about common gene lists Yes Yes Genes Yes