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

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

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.

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

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?

Cellular Component where a gene product acts

Cellular Component

Cellular Component

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

insulin receptor activity Molecular Function insulin binding insulin receptor activity

Biological Process a commonly recognized series of events cell division

Biological Process transcription

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. [http://cancerweb.ncl.ac.uk/omd/index.html] exact_synonym: glucose biosynthesis xref_analog: MetaCyc:GLUCONEO-PWY is_a: GO:0006006 is_a: GO:0006092 term name ontology definition 17800 terms in three ontologies 94% of terms defined synonym database ref parentage

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 

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

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

GO Annotation Database object GO term ID Reference for annotation gene or gene product GO term ID e.g. GO:0003677 Reference for annotation e.g. PubMed paper, BLAST results Evidence code (source of the annotation) from evidence code ontology

Functional enrichment analysis

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?

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.

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?

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) …

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.

BP Cellular process Cell division