1. a Cytoscape plugin to assess enrichment of
GO categories in biological networks
Steven Maere
5th Annual Cytoscape Retreat
Amsterdam, November 2007

2. Gene Ontology (GO)
GO provides three structured vocabularies to describe gene
function: biological process
- molecular function
- cellular component
Biological Process
Cell cycle
M phase
crosslinked, hierarchical
tree structure
level of detail increases with level in hierarchy
multiple annotations
per gene

3. BiNGO ?
Biological Network Gene Ontology tool : assess whether a given set of genes is significantly enriched in genes involved in particular functions/processes/pathways.
> 40 tools with similar functionality listed on GO website
Why BiNGO ? Its integration in Cytoscape provides several advantages :
BiNGO can be used interactively on molecular interaction graphs visualized in Cytoscape.
Integrated use of tools : BiNGO can be used in combination with other Cytoscape plugins (e.g. MCODE).
intuitive and versatile visualization of results
flexibility

4. BiNGO 2.0 Features
assesses overrepresentation or underrepresentation of GO categories in gene sets
Cytoscape or gene list input
batch mode : analyze several clusters simultaneously using same settings
GO and GOSlim ontologies, automated remapping of annotations
Wide range of organisms and gene identifiers
Evidence code filtering
Hypergeometric or binomial test for overrepresentation
Multiple testing correction using Bonferroni (FWER) or Benjamini&Hochberg (FDR) correction
Cytoscape visualization of results mapped on the GO hierarchy. 
extensive results in tab-delimited text file format
making and using custom annotation/ontology files is easy
open source

5. GO overrepresentation
x out of X genes in group A belong to GO category B which is shared by n out of N genes in the whole genome
genome : N
Group A : X
GO Cat B : n n x
we can use the hypergeometric distribution (a.k.a. the 2x2 exact Fisher test) to determine whether category B is significantly overrepresented in cluster A

6. Multiple testing correction
When testing multiple GO categories, a multiple testing correction has to be applied in order to control the false positive rate
Several strategies for adjusting p-values :
- controlling FWER = prob. of at least 1 type I error
e.g. Bonferroni correction
very conservative
- controlling the FDR = False Discovery Rate
controls % of false positives
e.g. Benjamini & Hochberg correction
valid for independent or + correlated tests
less conservative
Benjamini, Y. & Hochberg, Y., J. R. Statist. Soc. B 57(1), (1995)

7. BiNGO
DEMO

8. BiNGO
Maere S, Heymans K and Kuiper M (2005) BiNGO: a Cytoscape plugin to assess over-representation of Gene Ontology categories in biological networks. Bioinformatics 21,
Availability:
GO Tools at
Plugins at
Plugin Manager in Cytoscape
or Google ‘bingo gene ontology’

9. Thanks ! Karel Heymans, Martin Kuiper Ghent University
Andrew Markiel, Iliana Avila Institute for Systems Biology
Rowan Christmas
Ruth Isserlin, Gary Bader University of Toronto
Mike Smoot, Trey Ideker UC San Diego
Benno Schwikowski Institut Pasteur