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Protocols

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


No version available

Maintainer


  • person_outline Martin Kuiper

Additional information


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

Publication for BiNGO

BiNGO citations

 (341)
call_split

Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae

2018
Front Microbiol
PMCID: 5917014
PMID: 29725322
DOI: 10.3389/fmicb.2018.00752
call_split See protocol

[…] he target sequences were randomly generated () given a background model.Functional enrichment within the framework of Gene Ontology (GO) terms (positive or negative fold changes) was determined using BiNGO (). GO enrichment for differentially expressed genes is complicated by at an arbitrary fold-change cut-off imposed prior to the enrichment analysis, which excludes the genes with fold-change val […]

library_books

Effects of a community health promotion program on social factors in a vulnerable older adult population residing in social housing

2018
PMCID: 5902999
PMID: 29661136
DOI: 10.1186/s12877-018-0764-9

[…] d them from participating in future events, even after acknowledging that many improvements to the building had been made since CHAP-EMS/[email protected] was implemented. One participant described: “We play bingo every now and then. Before [another building resident] and them took it over it was just too much in-fighting. It was just terrible. They were all sniping at each other. Since they have done it, […]

library_books

Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle

2018
Sci Rep
PMCID: 5899093
PMID: 29654251
DOI: 10.1038/s41598-018-24341-y

[…] rmed using the cuffdiff tool of the cufflinks package. DEGs were identified based on a false discovery rate (FDR) < 0.05. Gene Ontology (GO) enrichment analysis was carried out on DEGs lists by using BiNGO and visualized with Cytoscape. We compared the transcriptional profile of the 089 treatment with the transcriptional profiles of A. fumigatus cells at different stages of the asexual cell cycle. […]

library_books

Transcriptome profiling reveals regulatory mechanisms underlying corolla senescence in petunia

2018
PMCID: 5878830
PMID: 29619227
DOI: 10.1038/s41438-018-0018-1

[…] eries expression miner (STEM) was used to cluster DEGs. The gene expression data and gene annotation files were uploaded to STEM. Expression profiles were analyzed using the STEM clustering algorithm.BiNGO 2.3 plugin tool in Cytoscape 3.2.1 was used to gain knowledge about gene ontology (GO) terms of DEGs in each cluster. Over-represented GO terms were identified using a hypergeometric test with a […]

call_split

Zeb1 Hdac2 eNOS circuitry identifies early cardiovascular precursors in naive mouse embryonic stem cells

2018
Nat Commun
PMCID: 5876398
PMID: 29599503
DOI: 10.1038/s41467-018-03668-0
call_split See protocol

[…] (Venny 2.1.0 [http://bioinfogp.cnb.csic.es/tools/venny/]). Gene ontology on genes exclusively regulated by NO (±2 log2 fold change, basemean >5, FDR <0.05) was performed using Cytoscape 3.2.1 plugin BINGO, which allows to determine statistically overrepresented GO categories in the derived biological networks. […]

library_books

Embryophyte stress signaling evolved in the algal progenitors of land plants

2018
Proc Natl Acad Sci U S A
PMCID: 5899452
PMID: 29581286
DOI: 10.1073/pnas.1719230115

[…] predicted a plastid (chloroplast) localization. Word clouds of any kind were generated using wordle.net in advanced settings. GO term enrichment was done based on eggNOG-mapper–assigned GO terms and BiNGO () with hypergeometric tests, Benjamini–Hochberg false discovery rate correction, and a custom reference annotation for each organism (based on all GO terms assigned to the reference transcripts […]

Citations

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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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