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BiNGO computational protocol

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

 (75)
2018
PMCID: 5796731
PMID: 29360820
DOI: 10.1371/journal.pgen.1007180

[…] deseq2 [163] 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 [164] in cytoscape v3.1.1 [165] with default parameters. the ontology terms and corresponding d. melanogaster annotations were downloaded from geneontology.org [166,167] (as of january 2015)., […]

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

[…] analysis [31] (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 [32], bingo [33], and revigo [34] 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: 5812550
PMID: 29444085
DOI: 10.1371/journal.pgen.1007234

[…] e: shows the significance level deviating from the random distribution between b73 and mo17. the go enrichments and the pathway enrichments of the regulated genes by hotspots were conducted using bingo plugin in cytoscape based on the annotation information from agrigo and maizecyc database, respectively. the results of go enrichments and pathway enrichments are in table s5 and table s6, […]

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

[…] 215 functional groups, respectively (tables s6a,b). twenty eight over-represented go terms of biological processes were found to be affected commonly in both ems and ms (table s6c). cytoscape plugin bingo was used to represent significantly overrepresented go terms in an enrichment network (figure 3). the top five shared biological process go terms were cell adhesion (go:0007155, 17 degs), […]

2018
PMCID: 5830583
PMID: 29491462
DOI: 10.1038/s41598-018-22237-5

[…] studied for each sub-network the enrichment in certain functional categories as defined by the go classification59. the gene set enrichment (gse) analysis was carried out using a combination of the bingo tool60 and the cytoscape software for visualization61. the enrichment test identifies the most abundant go terms in the sub-network compared to all the possible terms present in the complete […]

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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