BiNGO
Category Genomics>Gene Expression Analysis/Profiling/Tools
Abstract BiNGO (A Biological Network Gene Ontology tool) is a Java- based tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a sub-graph of a biological network.
BiNGO is implemented as a plug-in for Cytoscape (see G6G Abstract Number 20092), which is an open source bioinformatics software platform for visualizing and integrating molecular interaction networks.
BiNGO maps the predominant 'functional themes' of a given gene set on the GO hierarchy, and outputs this mapping as a Cytoscape graph.
Gene sets can either be selected or computed from a Cytoscape network (as sub-graphs) or compiled from sources other than Cytoscape (e.g. a list of genes that are significantly up-regulated in a 'microarray experiment').
The main advantage of BiNGO over other GO tools is the fact that it can be used directly and interactively on molecular interaction graphs.
Another plus is that BiNGO takes full advantage of Cytoscape's versatile visualization environment. This allows you to produce customized high- quality figures.
BiNGO features/capabilities include:
1) Assessing over-representation or under-representation of GO categories.
2) Graph or gene list input.
3) Batch mode: analyze several clusters simultaneously using the same settings.
4) Provides different GO and GO Slim ontologies ('GO slims' are cut- down versions of the GO ontologies containing a subset of the terms in the whole GO.
They give a broad overview of the ontology content without the detail of the specific fine grained terms).
5) Evidence code filtering.
6) BiNGO provides several default GO ontologies and annotations for a wide range of organisms.
The GO ontologies and annotations in BiNGO are parsed from information available at the National Center for Biotechnology Information (NCBI).
Updated versions will become available every six (6) months.
The identifiers supported in the default annotation files usually include Entrez Gene IDs, LocusTags, Official Gene Symbols and Unigene IDs, and other identifiers dependent on the organism.
7) Hyper-geometric or binomial test for over-representation.
8) Multiple testing corrections using Bonferroni Family-Wise Error Rate (FWER) or Benjamini & Hochberg False Discovery Rate (FDR) correction.
9) Interactive visualization of results mapped on the GO hierarchy. The ‘interactive visualization’ is the key to the interpretation of BiNGO results.
It would be hard to make the same interpretation in a reasonable amount of time based on textual output alone.
10) Provides more extensive results in tab-delimited text file format.
Next to the visual representation and BiNGO output window, BiNGO produces a tab-delimited text file containing more detailed results.
Apart from a listing of the analysis options, the results file contains the (adjusted) p-value for each over-represented GO class, the number of genes in the test set annotated to that class and their identity, and the number of genes annotated to that class in the reference set.
11) The ability to make and use your own annotation files. This feature is particularly useful if you want to:
- a) Use gene identifiers other than those provided in BiNGO (e.g. Affymetrix probe-sets).
- b) Use an annotation for an organism (e.g. Poplar) which is Not included in BiNGO.
- c) Test your set of genes against a custom reference set, e.g. all the genes on a microarray or in a large-scale Y2H (yeast two hybrid) screen.
- d) Use ontologies other than those provided, e.g. KEGG (Kyoto Encyclopedia of Genes and Genomes).
System Requirements
BiNGO is available as a platform-independent open-source Java application, released under the terms of the GPL.
Manufacturer
- Flanders Interuniversitary Institute for Biotechnology (VIB)
- Rijvisschestraat 120, B-9052
- Gent, Belgium
- phone: +32 9 244 66 11
- fax: +32 9 244 66 10
Manufacturer Web Site BiNGO
Price Contact manufacturer.
G6G Abstract Number 20281
G6G Manufacturer Number 101039