applications of go. goals of gene ontology project
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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– terms and definitions
2. Produce annotations to terms– gene product -> GO terms
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
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
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
Annotations to GO
Three key parts:
– gene name/id
Annotations to GO
Three key parts:
– gene name/id
– GO term
Annotations to GO
Three key parts:
– gene name/id
– GO term(s)
– evidence for association
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
Types of GO annotation:
Electronic Annotation
Manual Annotation
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
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
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
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
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
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
Inferred by Electronic Annotation
Annotation derived without human validation– mappings file e.g. interpro2go, ec2go.– Blast search ‘hits’
Lower ‘quality’ than experimental codes
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)
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
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
Databases
UniProtGOA-Human
GO
fly
yeast
worm
man
mouse rat
plants
parasite
bacteria
fishUniProtGOA-SPTRAll 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
Restricted view of the ontologies
Give broad view of gene function
Can be organism-specific or generic– plant– mammal– microbe
GO slims
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?
GO for microarray analysis
experimental condition
Gen
e
com
pone
nt
proc
ess
func
tion
The tutorial
Part I– Navigating GO and its annotations using
Part II– Analysing microarray data using GO with