1. GO : the Gene Ontology & Functional enrichment analysis
F. Burdet

2. Brief presentation of GO
Slides about GO used with the kind permission of:
Amelia Ireland
GO Curator
EBI, Cambridge, UK

3. What is the Gene Ontology?
Definition:
The Gene Ontology: “a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing”
A controlled vocabulary to describe gene products - proteins and RNA - in any organism.

4. What is GO? One of the Open Biological Ontologies
Standard, species-neutral way of representing biology
Three structured networks of defined terms to describe gene product attributes
More like a phrase book than a biology text book

5. How does GO work?
What does the gene product do?
Where and when does it act?
Why does it perform these activities?
What information might we want to capture about a gene product?

6. Cellular Component
where a gene product acts

7. Cellular Component

8. Cellular Component

9. Molecular Function activities or “jobs” of a gene product
glucose-6-phosphate isomerase activity

10. insulin receptor activity
Molecular Function
insulin binding
insulin receptor activity

11. Biological Process a commonly recognized series of events
cell division

12. Biological Process
transcription

13. Anatomy of a GO term unique GO ID id: GO:0006094 name: gluconeogenesis
namespace: process
def: The formation of glucose from
noncarbohydrate precursors, such as
pyruvate, amino acids and glycerol. [
exact_synonym: glucose biosynthesis
xref_analog: MetaCyc:GLUCONEO-PWY
is_a: GO:
is_a: GO:
term name
ontology
definition
17800 terms in three ontologies
94% of terms defined
synonym
database ref
parentage

14. Ontology Structure
Ontologies are structured as a hierarchical directed acyclic graph
Terms can have more than one parent and zero, one or more children
Terms are linked by two relationships
is-a 
part-of 

15. mitochondrial chloroplast
Ontology Structure
cell
membrane chloroplast
mitochondrial chloroplast
membrane membrane
is-a
part-of

16. GO Annotation
Using GO terms to represent the activities and localizations of a gene product
Annotations contributed by members of the GO Consortium
model organism databases
cross-species databases, eg. UniProt
Annotations freely available from GO website

17. GO Annotation Database object GO term ID Reference for annotation
gene or gene product
GO term ID
e.g. GO:
Reference for annotation
e.g. PubMed paper, BLAST results
Evidence code (source of the annotation)
from evidence code ontology

18. Functional enrichment analysis

19. An other way to look at the gene modules
I have a set of genes (from a module). On top of the correlations with the traits, can I discover more about it?
One way is to look if some known pathways or functionally related genes are enriched in this module
How can one assess the enrichment?

20. Example of the marbles (hypergeometric test)
Take an urn with 5 green and 45 red marbles
Draw 10 marbles randomly
What is the probability that 4 of the 10 are green?
=> use an hypergeometric test to calculate the probability !
And do the same with sets of genes (modules) found in a pathway, in comparison of a random draw of the same size across the whole set of genes.

21. From marbles to genes Say I have 100 genes in my orange module
25 out of the 30 genes involved in lipid biosynthesis are found in my orange module
Given the fact that there are 10’000 genes in the dataset…
What was the probability of this distribution to happen, compared to a random draw?

22. Biological databases available
Gene Ontology (GO)
KEGG (Kyoto Encyclopedia of Genes and Genomes)
Reactome
BioCarta
MSigDB (Molecular Signatures Database)
DAVID (Database for Annotation, Visualization and Integrated Discovery) …

23. topGO Bioconductor package
Has an algorithm that will only consider the significant “leaves” instead of all the levels (weight)
Usually, the gene universe is defined as all feasible genes measured by the microarray.

24. BP
Cellular process
Cell division