BiNGO pipeline

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 citations

 (26)
2018
PMCID: 5820528

[…] 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: 5812550

[…] 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, […]

2017
PMCID: 5698427

[…] for downstream analysis tpm was used as a measure of gene expression. a gene was considered detected if it had mean tpm >5., to assess the overrepresented go terms the cytoscape app bingo57 was used. statistical test used was hypergeometric test, benjamini–hochberg false discovery rate (fdr) correction was used to account for multiple tests and the significance level was set […]

2017
PMCID: 5577110

[…] methods with estimated absolute fold changes ≥ 1 and false discovery rates ≤ 0.01, were identified as reliable degs. functional enrichment analyses of these degs were performed using mapman46, bingo47, and kobas48. the transcriptomic analysis results were visualized using r (https://www.r-project.org/) and cytoscape software49. seventeen degs were randomly selected to validate the gene […]

2017
PMCID: 5559854

[…] discovery rate-adjusted p value) of <0.05 based on two independent biological replicates. go enrichment was performed using cytoscape software (http://www.cytoscape.org, version 2.5.2) with bingo plugin (http://www.psb.ugent.be/cbd/papers/bingo/, version 2.3). hypergeometric test with benjamini & hochberg false discovery rate (fdr) were performed using the default parameters […]

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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