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BiNGO specifications

Information


Unique identifier OMICS_04136
Name BiNGO
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 3.0.3
Stability Stable
Requirements
Cytoscape
Maintained Yes

Versioning


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Maintainer


  • person_outline Martin Kuiper <>

Additional information


Previous version : https://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

Publication for BiNGO

BiNGO in pipelines

 (183)
2018
PMCID: 5796731
PMID: 29360820
DOI: 10.1371/journal.pgen.1007180

[…] deseq2 [] library was used to normalize the background read count of the genes belonging to each cluster., the gene ontology terms enriched in each cluster of genes were obtained with the plugin bingo [] in cytoscape v3.1.1 [] with default parameters. the ontology terms and corresponding d. melanogaster annotations were downloaded from geneontology.org [,] (as of january 2015)., […]

2018
PMCID: 5797354
PMID: 29394946
DOI: 10.1186/s12957-018-1320-y

[…] encyclopedia of genes and genomes (kegg) pathways associated with the putative target genes were also analyzed in david. the results of go annotation and kegg pathway analysis were visualized using bingo and enrichmentmap plugins in cytoscape version 3.5.0. we used string (https://string-db.org/) to build interaction maps of the proteins encoded by the putative target genes., we selected […]

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

[…] enrichment analysis [] (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 […]

2018
PMCID: 5820528
PMID: 29503661
DOI: 10.3389/fgene.2018.00042

[…] on overlapping go-ids between ems and ms. the number of genes enclosed by sharing go terms was used to predict the significant pathways and ensuing crosstalk between these pathways. cytoscape plugin bingo (maere et al., ) and funrich v3 (pathan et al., ) stand alone software was separately used for functional enrichment analysis of degs., to expose the interactive associations among the degs […]

2018
PMCID: 5820528
PMID: 29503661
DOI: 10.3389/fgene.2018.00042

[…] 136 and 215 functional groups, respectively (tables ). twenty eight over-represented go terms of biological processes were found to be affected commonly in both ems and ms (table ). cytoscape plugin bingo was used to represent significantly overrepresented go terms in an enrichment network (figure ). the top five shared biological process go terms were cell adhesion (go:0007155, 17 degs), […]


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BiNGO in publications

 (865)
PMCID: 5945850
PMID: 29748583
DOI: 10.1038/s41598-018-25582-7

[…] nodes and 834 edges. detailed information on these hubs is provided in fig. . module analysis of protein interaction network had been conducted. as showed in fig. , 13 modules were identified. using bingo, the functions of the protein contained in the modules were annotated. each module’s biological process was shown in table . the module was graded according to the mcode algorithm. […]

PMCID: 5916944
PMID: 29695764
DOI: 10.1038/s41598-018-19919-5

[…] data to identify the genes co-expressing in at least two time points in either of the genotypes with a difference of 2 between their expression values. the resulting set of genes was analyzed with bingo to prepare a combined process map (supplementary fig. ). results showed that translation initiation and elongation seemed to be predominant in susceptible genotype while protein modification, […]

PMCID: 5915454
PMID: 29691375
DOI: 10.1038/s41398-018-0137-3

[…] al expressed genes were (i) separated in upregulated and downregulated genes; (ii) analyzed for full go overrepresentation according to hypergeometric testing with a significance cutoff fdr = 0.05 in bingo (version 3.0.3); (iii) processed with the enrichment map pipeline (https://f1000research.com/posters/5-1235) a p-value cutoff = 0.001, q-value cutoff = 0.05 and jaccard coefficient cutoff = 0.25 […]

PMCID: 5928201
PMID: 29740341
DOI: 10.3389/fphys.2018.00429

[…] used to find different clusters inside the network according to the number of connections between nodes. clusters were explored for their go biological process enrichment terms using the application bingo, filtering for results with a corrected q-value lower than 0.05 (benjamini hochberg correction)., an overview of the experimental design and applied methods is depicted in figure ., all horses […]

PMCID: 5908868
PMID: 29674689
DOI: 10.1038/s41598-018-24727-y

[…] mirnas and mrnas., gene-act network analysis was performed to identify the interactive network among the go terms enriched in mirnas negatively regulated by mrnas based on the go database using the bingo tool of cytoscape, which calculates overrepresented go terms in the network and displays them as a network of significant go terms. gene pathway network analysis was performed to identify […]


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BiNGO institution(s)
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Ghent, Belgium
BiNGO funding source(s)
Supported by the Fund for Scientific Research (Flanders, Belgium).

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