Transcript Applications of GO

Applications of GO
Goals of Gene Ontology Project
Goals of Gene Ontology Project
1.
Create controlled vocabularies
–
terms and definitions
Goals of Gene Ontology Project
1.
Create controlled vocabularies
–
2.
terms and definitions
Produce annotations to terms
–
gene product -> GO terms
Goals of Gene Ontology Project
1.
Create controlled vocabularies
–
2.
Produce annotations to terms
–
3.
terms and definitions
gene product -> GO terms
Produce GO tools
– browsing, searching and editing
Goals of Gene Ontology Project
1.
Create controlled vocabularies
–
2.
Produce annotations to terms
–
3.
terms and definitions
gene product -> GO terms
Produce GO tools
– browsing, searching and editing
•
Make everything publicly available
Annotations to GO
‘Gene associations’
 Associations between a gene/gene
product and GO terms
 Association made to each of the
ontologies
cellular component
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gene
product
biological process
molecular function
Annotations to GO
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Three key parts:
– gene name/id
Annotations to GO
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Three key parts:
– gene name/id
– GO term
Annotations to GO
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Three key parts:
– gene name/id
– GO term(s)
– evidence for association
Gene association file
SPTR
SPTR
SPTR
O00505
O00505
O00505
IMA3_HUMAN
IMA3_HUMAN
IMA3_HUMAN
Importin alpha-3 subunit
Importin alpha-3 subunit
Importin alpha-3 subunit
intracellular
protein transport
GO:0006886 GOA:interpro
GO:0005634 GOA:spkw
GO:0005643 PUBMED:9154134
IPI00012092
IPI00012092
IPI00012092
protein
protein
protein
nucleus
nuclear pore
IEA
IEA
TAS
taxon:9606
taxon:9606
taxon:9606
P
C
C
20020920 SPTR
20011011 SPTR
20020630 SPTR
Types of GO annotation:
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Electronic Annotation

Manual Annotation
Evidence types
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ISS: Inferred from Sequence/structural Similarity
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
IC: Inferred by Curator
ND: No Data available
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IEA: Inferred from electronic annotation
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Evidence types
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ISS: Inferred from Sequence/structural Similarity
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
IC: Inferred by Curator
ND: No Data available
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IEA: Inferred from electronic annotation
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Evidence types
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ISS: Inferred from Sequence/structural Similarity
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
IC: Inferred by Curator
ND: No Data available
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IEA: Inferred from electronic annotation
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Evidence types

ISS: Inferred from Sequence/structural Similarity
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
IC: Inferred by Curator
ND: No Data available
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IEA: Inferred from electronic annotation
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
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
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Evidence types

ISS: Inferred from Sequence/structural Similarity
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
IC: Inferred by Curator
ND: No Data available
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IEA: Inferred from electronic annotation
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
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



Evidence types

ISS: Inferred from Sequence/structural Similarity
IDA: Inferred from Direct Assay
IPI: Inferred from Physical Interaction
IMP: Inferred from Mutant Phenotype
IGI: Inferred from Genetic Interaction
IEP: Inferred from Expression Pattern
TAS: Traceable Author Statement
NAS: Non-traceable Author Statement
IC: Inferred by Curator
ND: No Data available
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IEA: Inferred from electronic annotation
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Inferred by Electronic Annotation
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Annotation derived without human
validation
– mappings file e.g. interpro2go, ec2go.
– Blast search ‘hits’
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Lower ‘quality’ than experimental codes
Mappings files
Fatty acid biosynthesis
( Swiss-Prot Keyword)
EC:6.4.1.2
(EC number)
GO:Fatty acid biosynthesis
(GO:0006633)
GO:acetyl-CoA carboxylase
activity
(GO:0003989)
IPR000438: Acetyl-CoA
carboxylase carboxyl
transferase beta subunit
(InterPro entry)
GO:acetyl-CoA carboxylase
activity
(GO:0003989)
Gene association file
SPTR
SPTR
SPTR
O00505
O00505
O00505
IMA3_HUMAN
IMA3_HUMAN
IMA3_HUMAN
Importin alpha-3 subunit
Importin alpha-3 subunit
Importin alpha-3 subunit
GO:0006886 GOA:interpro
GO:0005634 GOA:spkw
GO:0005643 PUBMED:9154134
IPI00012092
IPI00012092
IPI00012092
using an InterPro to GO
mappings file
protein
protein
protein
IEA
IEA
TAS
taxon:9606
taxon:9606
taxon:9606
P
C
C
20020920 SPTR
20011011 SPTR
20020630 SPTR
using a Swiss-Prot keyword
to GO mappings file
Submitting gene associations
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Many model organism databases
– Drosophila, mouse, Saccharomyces, rat,
zebrafish, prokaryotes, Arabidopsis, slime
mould, C. elegans, rice, parasites, viruses
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Swiss-Prot (UniProt)
– Associations for >8000 species including
human
Databases
mouse
rat
fly
yeast
man
GO
plants
UniProt
GOA-Human
parasite
bacteria
worm
fish
UniProt
GOA-SPTR
All Species
Finding GO terms
In this study, we report the isolation and molecular characterization
of the B. napus PERK1 cDNA, that is predicted to encode a novel
receptor-like kinase. We have shown that like other plant RLKs,
the kinase domain of PERK1 has serine/threonine kinase activity,
In addition, the location of a PERK1-GTP fusion protein to the
plasma membrane supports the prediction that PERK1 is an
integral membrane protein…these kinases have been implicated in
early stages of wound response…
GO slims
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Restricted view of the ontologies
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Give broad view of gene function
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Can be organism-specific or generic
– plant
– mammal
– microbe
GO slims
GO for microarray analysis
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Annotations give ‘function’ label to
genes
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Ask meaningful questions of microarray
data e.g.
– genes involved in the same process,
same/different expression patterns?
GO for microarray analysis
experimental condition
The tutorial
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Part I
– Navigating GO and its annotations using
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Part II
– Analysing microarray data using GO with