REViGO specifications

Information


Unique identifier OMICS_02283
Name REViGO
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

REViGO article

REViGO citations

 (8)
2018
PMCID: 5807917

[…] distribution using the r package topgo. the fdr of each go term was also calculated and listed in the supplementary table s1. go terms with enrichment analysis p-value ≤ 0.05 were taken as input for revigo., the metatranscriptome samples (in vivo samples) have been described previously (deng et al., 2017). they were derived from 14 individuals, four of which had been diagnosed with chronic […]

2018
PMCID: 5814942

[…] with the ontologizer (bauer et al. 2008) using the biological process subontology. enriched go terms are specified (supplementary tables s1 and s2, supplementary material online) and depicted by revigo (fig. 4; supek et al. 2011). the most significantly up-regulated go term in infected paramecia (fig. 4a) is lipid oxidation (including cellular lipid metabolism, cellular lipid catabolism, […]

2017
PMCID: 5791885

[…] < 0.01 and 30 for mingoterm (minimum count in a genome for a go term to be included). a bonferroni multiple hypothesis testing adjustment was finally applied to adjust the enrichment result. revigo online software was used to visualize summaries of the gene ontology analysis 50. medium was chosen for the simrel parameter., we have used a described pan-macroh2a1 antibody18 for chromatin […]

2017
PMCID: 5549995

[…] using the gostats package in r [42] and p-values of enriched terms were adjusted using the benjamini-hochberg method. redundancy in lists of significant go terms was reduced using the online tool revigo [43]. kegg pathway analysis was performed using david [44,45]., sample prep and sequencing: for 16s rdna high-throughput sequencing, we characterized a subset of samples used in the single […]

2016
PMCID: 4833139

[…] as previously described [55]. primer sequences are provided in supplemental table s1., david [56] was used for gene annotation, as well as enrichment analysis. to visualize go enrichments using revigo [57], we first translated go-terms to goslim using go:termfinder [58]. visualization for fig. 2 was done using cytoscape [59]., pathway enrichment analysis was done using the reactome fi […]

REViGO institution(s)
Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia

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