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Applications of GO
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Goals of Gene Ontology Project
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Goals of Gene Ontology Project
1. Create controlled vocabularies– terms and definitions
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Goals of Gene Ontology Project
1. Create controlled vocabularies– terms and definitions
2. Produce annotations to terms– gene product -> GO terms
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Goals of Gene Ontology Project
1. Create controlled vocabularies– terms and definitions
2. Produce annotations to terms– gene product -> GO terms
3. Produce GO tools– browsing, searching and editing
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Goals of Gene Ontology Project
1. Create controlled vocabularies– terms and definitions
2. Produce annotations to terms– gene product -> GO terms
3. Produce GO tools– browsing, searching and editing
• Make everything publicly available
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Annotations to GO
‘Gene associations’ Associations between a gene/gene
product and GO terms Association made to each of the
ontologies
gene product
cellular componentbiological processmolecular function
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Annotations to GO
Three key parts:
– gene name/id
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Annotations to GO
Three key parts:
– gene name/id
– GO term
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Annotations to GO
Three key parts:
– gene name/id
– GO term(s)
– evidence for association
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Gene association file
Importin alpha-3 subunit IPI00012092 protein taxon:9606 20020920 SPTRImportin alpha-3 subunit IPI00012092 protein taxon:9606 20011011 SPTRImportin alpha-3 subunit IPI00012092 protein taxon:9606 20020630 SPTR
SPTR O00505 IMA3_HUMAN GO:0006886 GOA:interpro IEA P
SPTR O00505 IMA3_HUMAN GO:0005634 GOA:spkw IEA C SPTR O00505 IMA3_HUMAN GO:0005643 PUBMED:9154134 TAS
C
intracellular
protein transport
nucleus
nuclear pore
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Types of GO annotation:
Electronic Annotation
Manual 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
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
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
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
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
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
IEA: Inferred from electronic annotation
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Inferred by Electronic Annotation
Annotation derived without human validation– mappings file e.g. interpro2go, ec2go.– Blast search ‘hits’
Lower ‘quality’ than experimental codes
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Mappings files
Fatty acid biosynthesis ( Swiss-Prot Keyword)
EC:6.4.1.2 (EC number)
IPR000438: Acetyl-CoA carboxylase carboxyl transferase beta subunit (InterPro entry)
GO:Fatty acid biosynthesis
(GO:0006633)
GO:acetyl-CoA carboxylase activity
(GO:0003989)
GO:acetyl-CoA carboxylaseactivity
(GO:0003989)
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Gene association file
Importin alpha-3 subunit IPI00012092 protein taxon:9606 20020920 SPTRImportin alpha-3 subunit IPI00012092 protein taxon:9606 20011011 SPTRImportin alpha-3 subunit IPI00012092 protein taxon:9606 20020630 SPTR
SPTR O00505 IMA3_HUMAN GO:0006886 GOA:interpro IEA P
SPTR O00505 IMA3_HUMAN GO:0005634 GOA:spkw IEA C SPTR O00505 IMA3_HUMAN GO:0005643 PUBMED:9154134 TAS
C
using an InterPro to GO mappings file
using a Swiss-Prot keyword to GO mappings file
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Submitting gene associations
Many model organism databases– Drosophila, mouse, Saccharomyces, rat,
zebrafish, prokaryotes, Arabidopsis, slime mould, C. elegans, rice, parasites, viruses
Swiss-Prot (UniProt)– Associations for >8000 species including
human
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Databases
UniProtGOA-Human
GO
fly
yeast
worm
man
mouse rat
plants
parasite
bacteria
fishUniProtGOA-SPTRAll Species
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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…
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GO slims
Restricted view of the ontologies
Give broad view of gene function
Can be organism-specific or generic– plant– mammal– microbe
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GO slims
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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?
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GO for microarray analysis
experimental condition
Gen
e
com
pone
nt
proc
ess
func
tion
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The tutorial
Part I– Navigating GO and its annotations using
Part II– Analysing microarray data using GO with