REViGO protocols

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REViGO specifications

Information


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

Publication for REViGO

REViGO in pipelines

 (87)
2018
PMCID: 5797081
PMID: 29396481
DOI: 10.1038/s41598-018-20457-3

[…] mf), the semantic similarity of the top 50 go terms was computed, after filtering for p-value < 0.01 and a number of associated genes >1 and <50 was identified and visualised with the revigo webtool (http://revigo.irb.hr/). the go term number and ranking score were used as the input., intersections between sets of clusters were computed with the “intersectbed” tool […]

2018
PMCID: 5801803
PMID: 29409495
DOI: 10.1186/s13045-018-0560-1

[…] [] (gsea) was employed to demonstrate the association between our genes of interest and defined gene sets. the gene annotation network analysis was performed using the gather [], bingo [], and revigo [] software., this study was approved by the institutional review board of peking university people’s hospital. blood samples were collected from donors with written informed consent. npg mice […]

2018
PMCID: 5807917
PMID: 29467738
DOI: 10.3389/fmicb.2018.00124

[…] distribution using the r package topgo. the fdr of each go term was also calculated and listed in the supplementary table . 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 (). they were derived from 14 individuals, four of which had been diagnosed with chronic periodontitis. […]

2018
PMCID: 5821092
PMID: 29440571
DOI: 10.1128/mBio.01939-17

[…] up- and downregulated genes (adjusted p value of <0.05) between every consecutive pair of conditions. the resulting lists of significantly overrepresented go terms were trimmed using revigo ()., to identify coexpressed gene clusters on the genome, a sliding window analysis was performed using croc software (). for the sliding window, a step size of one gene and a window size […]

2018
PMCID: 5883146
PMID: 29643862
DOI: 10.3389/fpls.2018.00401

[…] , www.eggplantgenome.org , www.eggplantmicrosatellite.org/ , http://kofler.or.at/bioinformatics/sciroko , http://bedtools.readthedocs.io , http://systemsbiology.cau.edu.cn/agrigov2/ , revigo.irb.hr/ , https://sourceforge.net/projects/primer3 , www.artichokegenome.unito.it/cymsatdb/ , the supplementary material for this article can be found online at: […]


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REViGO in publications

 (569)
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] the gage r tool. clustering was performed by principal component analysis and hierarchical clustering. gene ontology analyses were performed by david (https://david.ncifcrf.gov/) and visualized by revigo (http://revigo.irb.hr/). the tophat-fusion tool was used for the detection of fusion gene loci., a total of 6,251 viral genomes were obtained […]

PMCID: 5930835
PMID: 29743927
DOI: 10.1186/s12983-018-0252-2

[…] relevant candidate genes and enrichment results for tpa detoxification and cold hardiness in h. euphorbiae.table 3go terms (biological process and molecular function) are grouped according to revigo semantic categories [] and generic go slim terms, go terms (biological process and molecular function) are grouped according to revigo semantic categories [] and generic go slim terms, […]

PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] of the query sequences was analyzed using funfhmmer http://www.cathdb.info/search/by_funfhmmer web server [] to evaluate their functional annotations based on gene ontological terms. further, the revigo analysis, based on a hypergeometric distribution test was performed by fetching the identified go ids for characterizing their functional dimension on scattered plots using the revigo web […]

PMCID: 5932338
PMID: 29755439
DOI: 10.3389/fmicb.2018.00818

[…] reported, the p-value was calculated and subjected to benjamini-hochberg correction, with adjusted p-values ≤ 0.05 as a threshold. in addition, we summarized and visualized the go terms employing revigo (; )., a previous study has shown that the rnai components not involved in vegetative development and pathogenesis in f. graminearum (). therefore, we analyzed the expression patterns of fgdcl […]

PMCID: 5925605
PMID: 29740534
DOI: 10.3389/fonc.2018.00100

[…] p-value <0.01 were considered significant. only the biological processes were reported. the redundant go terms were reduced, and following a multiple dimensional scaling, visualized using revigo tool (). the relationships across the significant go terms were plotted in a hierarchical order using gorilla tool ()., we used epimod algorithm () to search for the “interactome hotspots” […]


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

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