Download - Gene Ontology (GO) Project Jane Lomax
http://www.geneontology.org/Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...
Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)
attacked
time
control
Puparial adhesionMolting cyclehemocyanin
Defense responseImmune responseResponse to stimulusToll regulated genesJAK-STAT regulated genes
Immune responseToll regulated genes
Amino acid catabolismLipid metobolism
Peptidase activityProtein catabloismImmune response
Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...
Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)
Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.
Microarray datashows changed expression ofthousands of genes.
How will you spot the patterns?
http://www.geneontology.org/
The Gene Ontology provides a way to capture and represent biological all this knowledge in a computable form
http://www.geneontology.org/
Definition of mesodermdevelopment
Gene productsinvolved in mesodermdevelopment
http://www.geneontology.org/
Microarray process:
• Treat samples• Collect mRNA• Label• Hybridize• Scan• Normalize• Select differentially regulated genes • Understand the biological phenomena involved
http://www.geneontology.org/
Traditional analysis
• gene by gene basis
• requires literature searching
• time-consuming
http://www.geneontology.org/
Traditional analysisGene 1ApoptosisCell-cell signalingProtein phosphorylationMitosis…
Gene 2Growth controlMitosisOncogenesisProtein phosphorylation…
Gene 3Growth controlMitosisOncogenesisProtein phosphorylation…
Gene 4Nervous systemPregnancyOncogenesisMitosis…
Gene 100Positive ctrl. of cell prolifMitosisOncogenesisGlucose transport…
http://www.geneontology.org/
Using GO annotations
• But by using GO annotations, this work has already been done
GO:0006915 : apoptosis
http://www.geneontology.org/
Grouping by process
ApoptosisGene 1Gene 53
MitosisGene 2Gene 5Gene45Gene 7Gene 35…
Positive ctrl. of cell prolif.Gene 7Gene 3Gene 12…
GrowthGene 5Gene 2Gene 6…
Glucose transportGene 7Gene 3Gene 6…
http://www.geneontology.org/
GO for microarray analysis
• Annotations give ‘function’ label to genes
• Ask meaningful questions of microarray data e.g.– genes involved in the same process,
same/different expression patterns?
http://www.geneontology.org/
GO structure• GO isn’t just a flat list
of biological terms• terms are related
within a hierarchy
http://www.geneontology.org/
GO structure
• This means genes can be grouped according to user-defined levels
• Allows broad overview of gene set or genome
http://www.geneontology.org/
How does GO work?
What information might we want to capture about a gene product?What information might we want to capture about a gene product?
http://www.geneontology.org/
How does GO work?
• What does the gene product do?
What information might we want to capture about a gene product?What information might we want to capture about a gene product?
http://www.geneontology.org/
How does GO work?
• What does the gene product do?• Where and when does it act?
What information might we want to capture about a gene product?What information might we want to capture about a gene product?
http://www.geneontology.org/
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?What information might we want to capture about a gene product?
http://www.geneontology.org/
GO structure
• GO terms divided into three parts:– cellular component– molecular function– biological process
http://www.geneontology.org/
Cellular Component
• Enzyme complexes in the component ontology refer to places, not activities.
http://www.geneontology.org/
Molecular Function
• activities or “jobs” of a gene product
glucose-6-phosphate isomerase activity
http://www.geneontology.org/
Molecular Function
• A gene product may have several functions; a function term refers to a reaction or activity, not a gene product
• Sets of functions make up a biological process
http://www.geneontology.org/
Biological Process
a commonly recognized series of events
cell division
http://www.geneontology.org/
Ontology Structure
• Terms are linked by two relationships– is-a – part-of
http://www.geneontology.org/
Ontology Structurecell
membrane chloroplast
mitochondrial chloroplastmembrane membrane
is-apart-of
http://www.geneontology.org/
Ontology Structure
• Ontologies are structured as a hierarchical directed acyclic graph (DAG)
• Terms can have more than one parent and zero, one or more children
http://www.geneontology.org/
Ontology Structure
cell
membrane chloroplast
mitochondrial chloroplastmembrane membrane
Directed Acyclic Graph (DAG) - multiple
parentage allowed
http://www.geneontology.org/
Anatomy of a GO termid: GO:0006094name: gluconeogenesisnamespace: processdef: The formation of glucose fromnoncarbohydrate precursors, such aspyruvate, amino acids and glycerol.[http://cancerweb.ncl.ac.uk/omd/index.html]exact_synonym: glucose biosynthesisxref_analog: MetaCyc:GLUCONEO-PWYis_a: GO:0006006is_a: GO:0006092
unique GO IDterm name
definition
synonymdatabase ref
parentage
ontology
http://www.geneontology.org/
GO can also be useful for resolving language conflicts amongst scientific communities
http://www.geneontology.org/
= tooth bud initiation
= cellular bud initiation
= flower bud initiation
http://www.geneontology.org/
Categorization of gene productsusing GO is called annotation.
So how does that happen?
http://www.geneontology.org/
P05147 PMID: 2976880
GO:0047519
Find the GO term describing itsfunction, process or location of action.
http://www.geneontology.org/
P05147
PMID: 2976880
GO:0047519
IDA
P05147 GO:0047519 IDA PMID:2976880
Record these:
http://www.geneontology.org/
Clark et al., 2005
Many species groups annotate
We see the research of one function across all species
http://www.geneontology.org/
Developing GO
• GO under constant development• International group of developers
– central editorial office at EBI - 4 members
• Developed in consultation with domain experts– Term suggestions handled through online
tracking system
http://www.geneontology.org/
2006 Consortium Meeting,
St. Croix,
U.S. Virgin Islands, March 30 - April 3, 2006
http://www.geneontology.org/
Contributors
dictyBase FlyBase GeneDB Gramene
Reactome WormBase The GO Editorial Office
Berkeley Bioinformatics and Ontology Project (BBOP)
Gene Ontology Annotation @ EBI (GOA)
Mouse Genome Database (MGD) and Gene Expression Database (GXD)
Rat Genome Database (RGD)
Saccharomyces Genome Database (SGD)
The Arabidopsis Information Resource (TAIR)
The Institute for Genomic Research (TIGR)
Zebrafish Information Network (ZFIN)