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Gene Ontology
Project
http://www.geneontology.org/
There is a lot
of biological
research output.
Search on
mesoderm
development…
You get 6752
results!
How will you
ever find what
you want?
Another
example…
time
Microarray data
shows changed
expression of
Defense response
thousands of genes.
Immune response
Response to stimulus
Toll regulated genes
JAK-STAT regulated genes
How will you spot
the patterns?
Amino acid catabolism
Puparial adhesion
Molting cycle
hemocyanin
Lipid metobolism
Peptidase activity
Protein catabloism
Immune response
Immune response
Toll regulated genes
Bregje Wertheim at the Centre for Evolutionary Genomics,
attacked control
Department of Biology, UCL and Eugene Schuster Group, EBI.
Selected Gene
Tree:
pearson
Coloredby:
by:
ne Tree:
pearson
lw n3d
... lw n3d ... Colored
Branch color
classification:
Set_LW_n3d_5p_...
Gene
List:
classification:
Set_LW_n3d_5p_...
Gene
List:
Copy
of Copy
C5_RMA
Copy
ofofCopy
of(Defa...
C5_RMA (Defa...
allall
genes
(14010)(14010)
genes
Scientists
work hard.
http://www.teamtechnology.co.uk/f-scientist.jpg
http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif
There are
lots of papers
to read.
http://www.teamtechnology.co.uk/f-scientist.jpg
http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif
More papers…
http://www.teamtechnology.co.uk/f-scientist.jpg
http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif
more and
more
and more!
http://www.teamtechnology.co.uk/f-scientist.jpg
http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif
more and
more
and more!
Help!
http://www.teamtechnology.co.uk/f-scientist.jpg
Aiuto!
http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif
Can the computer
geeks help?
They are trying!
http://www.newberntg.com/images/Computer-Geek-2.gif
With ontologies!
Ontology is a way to capture
knowledge in a written and
computable form.
computable
The computer finds patterns
so we don’t have to.
The Gene Ontology
This is our
browser.
Search on
mesoderm
development.
Here is
mesoderm
development.
Definition of
mesoderm
development.
Gene products
involved in
mesoderm
development.
There are many
gene products
involved in
mesoderm
development.
But fewer gene
products than
papers.
You can read
papers describing
what is known
about them.
Gene Ontology can help with Microarray data.
time
Defense response
Immune response
Response to stimulus
Toll regulated genes
JAK-STAT regulated genes
Puparial adhesion
Molting cycle
hemocyanin
Amino acid catabolism
Lipid metobolism
Peptidase activity
Protein catabloism
Immune response
Immune response
Toll regulated genes
Bregje Wertheim at the Centre for Evolutionary Genomics,
attacked control
Department of Biology, UCL and Eugene Schuster Group, EBI.
Selected Gene
Tree:
pearson
Coloredby:
by:
ne Tree:
pearson
lw n3d
... lw n3d ... Colored
Branch color
classification:
Set_LW_n3d_5p_...
Gene
List:
classification:
Set_LW_n3d_5p_...
Gene
List:
Copy
of Copy
C5_RMA
Copy
ofofCopy
of(Defa...
C5_RMA (Defa...
allall
genes
(14010)(14010)
genes
See which processes are upregulated or downregulated.
time
Defense response
Immune response
Response to stimulus
Toll regulated genes
JAK-STAT regulated genes
Puparial adhesion
Molting cycle
hemocyanin
Amino acid catabolism
Lipid metobolism
Peptidase activity
Protein catabloism
Immune response
Immune response
Toll regulated genes
Bregje Wertheim at the Centre for Evolutionary Genomics,
attacked control
Department of Biology, UCL and Eugene Schuster Group, EBI.
Selected Gene
Tree:
pearson
Coloredby:
by:
ne Tree:
pearson
lw n3d
... lw n3d ... Colored
Branch color
classification:
Set_LW_n3d_5p_...
Gene
List:
classification:
Set_LW_n3d_5p_...
Gene
List:
Copy
of Copy
C5_RMA
Copy
ofofCopy
of(Defa...
C5_RMA (Defa...
allall
genes
(14010)(14010)
genes
Whole genome analysis
(J. D. Munkvold et al., 2004)
How does the
Gene Ontology work?
Clark et al., 2005
A diagram
of the
whole system.
is_a
part_of
The Gene Ontology
is like a dictionary
Each
concept has:
• a name
• a definition
• an ID number
term: transcription initiation
id: GO:0006352
definition: Processes involved
in the assembly of the RNA
polymerase complex at the
promoter region of a DNA
template resulting in the
subsequent synthesis of
RNA from that promoter.
The ontologies are used to categorize gene products.
• Biological process ontology
Which process is a gene product involved in?
• Molecular function ontology
Which molecular function does a gene product have?
• Cellular component ontology
Where does a gene product act?
An example…
Mitochondrial P450
(CC24 PR01238; MITP450CC24)
Where is it?
Mitochondrial
p450
mitochondrial inner
membrane
GO cellular component term:
GO:0005743
What does it do?
substrate + O2 = CO2 +H20 product
monooxygenase activity
GO molecular function term:
GO:0004497
Which process is this?
electron transport
http://ntri.tamuk.edu/cell/
mitochondrion/krebpic.html
GO biological process term:
GO:0006118
Molecular function ontology
Nucleic acid binding is a
type of binding.
is_a
is_a
DNA binding is a type of
nucleic acid binding.
Biological process ontology
Adaxial/abaxial pattern
formation is a type of
pattern specification.
is_a
is_a
part_of
Adaxial/abaxial pattern
specification is a part of
adaxial/abaxial pattern
formation.
Cellular component ontology
is_a
membranebound
organelle is a
type of
organelle
nucleus is part
of the
intracellular
domain
part_of
Categorizing gene products is called ‘annotation’.
process
function
component
The gene product inner no
outer is involved in
adaxial/abaxial
axis specification.
process
function
component
The gene product inner no outer
has transcription factor activity.
process
function
component
The gene product inner no outer
is active in the nucleus.
Clark et al., 2005
A diagram
of the
whole system.
is_a
part_of
Clark et al., 2005
Many species
groups annotate.
We see the
research of one
function across
all species.
The Gene Ontology is for all species
and that means
we have to
*bridge*
some language barriers.
Same name, same thing?
http://www.darknessandlight.co.uk/cambridge_photographs.html
Bridge of Sighs,
Cambridge.
http://www.lockeheemstra.com/italy/bridge-of-sighs-venice.html
Ponte dei Sospiri,
Venice.
In biology…
Tactition
Taction
Tactile sense
?
Tactition
Taction
Tactile sense
perception of touch ; GO:0050975
Bud initiation?
An imaginary
example.
tooth bud initiation
broad_synonym: bud initiation
reproductive bud initiation
broad_synonym: bud initiation
shoot bud initiation
broad_synonym: bud initiation
Categorization of gene products
using GO is called annotation.
So how does that happen?
P05147
Choose your
favourite gene.
P05147
Find a paper
about it.
PMID: 2976880
P05147
PMID: 2976880
Find the GO
term describing its
function, process
or location of action.
GO:0047519
P05147
PMID: 2976880
What
evidence
do they
show?
IDA
GO:0047519
P05147
PMID: 2976880
Write these down…
P05147
GO:0047519
IDA
PMID:2976880
IDA
GO:0047519
Send to the GO Consortium.
Annotation appears in AmiGO.
GO slims
Clark et al., 2005
is_a
part_of
Clark et al., 2005
is_a
part_of
Whole genome analysis
(J. D. Munkvold et al., 2004)
…analysis of high-throughput data according to GO
MicroArray data analysis
time
Defense response
Immune response
Response to stimulus
Toll regulated genes
JAK-STAT regulated genes
Puparial adhesion
Molting cycle
hemocyanin
Amino acid catabolism
Lipid metobolism
Peptidase activity
Protein catabloism
Immune response
Immune response
Toll regulated genes
attacked control
cted Gene
Tree:
pearson
Coloredby:
by:
pearson
lw n3d
... lw n3d ... Colored
nch color
classification:
Set_LW_n3d_5p_...
Gene
List:
Set_LW_n3d_5p_...
Gene
List:
Bregje Wertheim at the Centre for Evolutionary Genomics,
Department of Biology, UCL and Eugene Schuster Group, EBI.
Copy
of Copy
C5_RMA
Copy
ofofCopy
of(Defa...
C5_RMA (Defa...
allall
genes
(14010)(14010)
genes
Adding terms
to the GO.
2006 Consortium Meeting,
St. Croix,
U.S. Virgin Islands, March 30 - April 3, 2006
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)