REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

By Fran Supek, Matko Bosnjak, Nives Skunca, Tomislav Smuc. 2011

5,771 citations recorded by the source corpus.

Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret. REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views. REVIGO is freely available at http://revigo.irb.hr/.

Subfields: Molecular Biology

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Citations in the corpus

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes (2018, background): “These and other terms can be taken to an external REViGO website [32] by clicking on the Open in Revigo button.”
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) (2019, methodology): “The enrichment results were then visualized using REVIGO (35).”
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update (2018, methodology): “Some tools were created to carry out these analyses, such as agriGO 2.0 (16), BiNGO (17), g:Profiler (18), Gorilla (19), etc. (20,21).”
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center (2021, background): “GO enrichment data can also be exported to REVIGO (22), facilitating data visualisation through a range of interactive tools including treemaps and graphs.”
A benchmark of gene expression tissue-specificity metrics (2015, methodology): “Gene Ontology enrichment analysis was performed with GOrilla (Eden et al. 2009) and Revigo (Supek et al. 2011).”
Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast (2013, methodology): “…(GO) searches for Biological Process and Cellular Component the different categories enriched in the changes of HL, nTR, Xrn1 binding and responsiveness were done using the online GOrilla tool (Eden et al., 2009), and the data obtained were filtered with the online ReViGO tool (Supek et al., 2011).”