Using%20The%20Gene%20Ontology:

1
Using The Gene Ontology
Gene Product Annotation
2
GO Project Goals

• Compile structured vocabularies describing
• aspects of molecular biology
• Describe gene products using vocabulary terms
• (annotation)
• Develop tools
• to query and modify the vocabularies and
• annotations
• annotation tools for curators

3
GO Data

• GO provides two bodies of data
• Terms with definitions and cross-
• references
• Gene product annotations with
• supporting data

4
The Three Ontologies

• Molecular Function elemental activity or task
• nuclease, DNA binding, transcription factor
• Biological Process broad objective or goal
• mitosis, signal transduction, metabolism
• Cellular Component location or complex
• nucleus, ribosome, origin recognition complex

5
DAG Structure
Directed acyclic graph each child may have one
or more parents
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The True Path Rule
Every path from a node back to the root must be
biologically accurate
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GO Annotation

• Association between gene product and
• applicable GO terms
• Provided by member databases
• Made by manual or automated methods

8
DAG Structure
Annotate to any level within DAG
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DAG Structure
mitotic chromosome condensation S.c. BRN1, D.m.
barren
Annotate to any level within DAG
10
DAG Structure
mitosis S.c. NNF1
mitotic chromosome condensation S.c. BRN1, D.m.
barren
Annotate to any level within DAG
11
GO Annotation Data

• Database object gene or gene product
• GO term ID
• Reference
• publication or computational method
• Evidence supporting annotation

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GO Evidence Codes
IDA - Inferred from Direct Assay IMP - Inferred
from Mutant Phenotype IGI - Inferred from
Genetic Interaction IPI - Inferred from
Physical Interaction IEP - Inferred from
Expression Pattern
TAS - Traceable Author Statement NAS -
Non-traceable Author Statement IC - Inferred by
Curator ISS - Inferred from Sequence or
structural Similarity IEA - Inferred from
Electronic Annotation ND - Not Determined
13
GO Evidence Codes
IDA - Inferred from Direct Assay IMP - Inferred
from Mutant Phenotype IGI - Inferred from
Genetic Interaction IPI - Inferred from
Physical Interaction IEP - Inferred from
Expression Pattern
TAS - Traceable Author Statement NAS -
Non-traceable Author Statement IC - Inferred by
Curator ISS - Inferred from Sequence or
structural Similarity IEA - Inferred from
Electronic Annotation ND - Not Determined
From primary literature
14
GO Evidence Codes
From reviews or introductions
IDA - Inferred from Direct Assay IMP - Inferred
from Mutant Phenotype IGI - Inferred from
Genetic Interaction IPI - Inferred from
Physical Interaction IEP - Inferred from
Expression Pattern
TAS - Traceable Author Statement NAS -
Non-traceable Author Statement IC - Inferred by
Curator ISS - Inferred from Sequence or
structural Similarity IEA - Inferred from
Electronic Annotation ND - Not Determined
From primary literature
15
GO Evidence Codes
From reviews or introductions
IDA - Inferred from Direct Assay IMP - Inferred
from Mutant Phenotype IGI - Inferred from
Genetic Interaction IPI - Inferred from
Physical Interaction IEP - Inferred from
Expression Pattern
TAS - Traceable Author Statement NAS -
Non-traceable Author Statement IC - Inferred by
Curator ISS - Inferred from Sequence or
structural Similarity IEA - Inferred from
Electronic Annotation ND - Not Determined
From primary literature
16
GO Evidence Codes
From reviews or introductions
IDA - Inferred from Direct Assay IMP - Inferred
from Mutant Phenotype IGI - Inferred from
Genetic Interaction IPI - Inferred from
Physical Interaction IEP - Inferred from
Expression Pattern
TAS - Traceable Author Statement NAS -
Non-traceable Author Statement IC - Inferred by
Curator ISS - Inferred from Sequence or
structural Similarity IEA - Inferred from
Electronic Annotation ND - Not Determined
automated
From primary literature
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GO Annotation Methods

• Manual
• Automated
• sequence similarity
• transitive annotation
• nomenclature, other text matching

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Literature-Based Manual Annotation Experimental
Evidence Codes
Lecoq, K., et al. (2001) YLR209C Encodes
Saccharomyces cerevisiae Purine Nucleoside
Phosphorylase. J. Bacteriology 183(16) 4910-4913.
Experiment 1 - Purification and enzyme
assay Purified His-tagged Ylr209cp can convert
various nucleoside substrates to bases Pi
inosine and guanosine are substrates Experiment
2 - Knockout of YLR209C null mutant excretes
inosine and guanosine into medium (compounds in
medium separated by chromatography and identified
by HPLC separation profiles)
19
Literature-Based Manual Annotation Experimental
Evidence Codes
Lecoq, K., et al. (2001) YLR209C encodes
Saccharomyces cerevisiae purine nucleoside
phosphorylase. J. Bacteriol. 183(16) 49104913.
Experiment 1 - Purification and enzyme
assay Purified His-tagged Ylr209cp can convert
various nucleoside substrates to bases Pi
inosine and guanosine are substrates Experiment
2 - Knockout of YLR209C null mutant excretes
inosine and guanosine into medium (compounds in
medium separated by chromatography and identified
by HPLC separation profiles)
IDA
20
Literature-Based Manual Annotation Experimental
Evidence Codes
Lecoq, K., et al. (2001) YLR209C encodes
Saccharomyces cerevisiae purine nucleoside
phosphorylase. J. Bacteriol. 183(16) 49104913.
FUNCTION
Experiment 1 - Purification and enzyme
assay Purified His-tagged Ylr209cp can convert
various nucleoside substrates to bases Pi
inosine and guanosine are substrates Experiment
2 - Knockout of YLR209C null mutant excretes
inosine and guanosine into medium (compounds in
medium separated by chromatography and identified
by HPLC separation profiles)
IDA
purine nucleoside phosphorylase
21
Literature-Based Manual Annotation Experimental
Evidence Codes
Lecoq, K., et al. (2001) YLR209C ncodes
Saccharomyces cerevisiae purine nucleoside
phosphorylase. J. Bacteriol. 183(16) 49104913.
FUNCTION
Experiment 1 - Purification and enzyme
assay Purified His-tagged Ylr209cp can convert
various nucleoside substrates to bases Pi
inosine and guanosine are substrates Experiment
2 - Knockout of YLR209C null mutant excretes
inosine and guanosine into medium (compounds in
medium separated by chromatography and identified
by HPLC separation profiles)
IDA
purine nucleoside phosphorylase
IMP
22
Literature-Based Manual Annotation Experimental
Evidence Codes
Lecoq, K., et al. (2001) YLR209C encodes
Saccharomyces cerevisiae purine nucleoside
phosphorylase. J. Bacteriol. 183(16) 49104913.
FUNCTION
Experiment 1 - Purification and enzyme
assay Purified His-tagged Ylr209cp can convert
various nucleoside substrates to bases Pi
inosine and guanosine are substrates Experiment
2 - Knockout of YLR209C null mutant excretes
inosine and guanosine into medium (compounds in
medium separated by chromatography and identified
by HPLC separation profiles)
IDA
purine nucleoside phosphorylase
IMP
23
Literature-Based Manual Annotation Experimental
Evidence Codes
Lecoq, K., et al. (2001) YLR209C encodes
Saccharomyces cerevisiae purine nucleoside
phosphorylase. J. Bacteriol. 183(16) 49104913.
FUNCTION
Experiment 1 - Purification and enzyme
assay Purified His-tagged Ylr209cp can convert
various nucleoside substrates to bases Pi
inosine and guanosine are substrates Experiment
2 - Knockout of YLR209C null mutant excretes
inosine and guanosine into medium (compounds in
medium separated by chromatography and identified
by HPLC separation profiles)
IDA
purine nucleoside phosphorylase
PROCESS
purine nucleoside catabolism
IMP
24
Literature-Based Manual Annotation Experimental
Evidence Codes
Lecoq, K., et al. (2001) YLR209C encodes
Saccharomyces cerevisiae purine nucleoside
phosphorylase. J. Bacteriol. 183(16) 49104913.
FUNCTION
Experiment 1 - Purification and enzyme
assay Purified His-tagged Ylr209cp can convert
various nucleoside substrates to bases Pi
inosine and guanosine are substrates Experiment
2 - Knockout of YLR209C null mutant excretes
inosine and guanosine into medium (compounds in
medium separated by chromatography and identified
by HPLC separation profiles)
IDA
purine nucleoside phosphorylase
PROCESS
purine nucleoside catabolism
IMP
This paper has no data for cellular component.
25
Automated Annotation InterPro Example
InterPro entry
GO entry
InterPro2go links InterPro entries and GO terms
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Automated Annotation InterPro Example
Run InterProScan to link YFP and InterPro entry
InterPro entry
GO entry
InterPro2go links InterPro entries and GO terms
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Automated Annotation InterPro Example
Run InterProScan to link YFP and InterPro entry
Infer GO term from the other two links
InterPro entry
GO entry
InterPro2go links InterPro entries and GO terms
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AmiGO Browser
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AmiGO Browser
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GO Annotation Contributors

• FlyBase WormBase
• Saccharomyces Genome Database DictyBase
• Mouse Genome Informatics Gramene
• The Arabidopsis Information Resource Compugen,
  Inc.
• Swiss-Prot/TrEMBL/InterPro
• Pathogen Sequencing Unit (Sanger Institute)
• PomBase (Sanger Institute)
• Rat Genome Database
• The Institute for Genomic Research

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GO Annotation Organisms

• Fruit fly (Drosophila melanogaster)
• Budding yeast (Saccharomyces cerevisiae)
• Fission yeast (Schizosaccharomyces pombe)
• Human (Homo sapiens)
• Mouse (Mus musculus) Rice (Oryza sativa)
• Rat (Rattus norvegicus) Tsetse fly (G.
  morsitans)
• Caenorhabditis elegans Arabidopsis thaliana
• Vibrio cholerae Dictyostelium discoideum

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Current GO Annotations
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www.geneontology.org

• FlyBase Berkeley Drosophila Genome Project
  WormBase
• Saccharomyces Genome Database DictyBase
• Mouse Genome Informatics Gramene
• The Arabidopsis Information Resource
  Compugen, Inc.
• Swiss-Prot/TrEMBL/InterPro
• Pathogen Sequencing Unit (Sanger Institute)
• PomBase (Sanger Institute)
• Rat Genome Database
• Genome Knowledge Base (CSHL)
• The Institute for Genomic Research

The Gene Ontology Consortium is supported by
NHGRI grant HG02273 (R01). The Gene Ontology
project thanks AstraZeneca for financial support.
The Stanford group acknowledges a gift from
Incyte Genomics.
34
Conference Standards and Ontologies for
Functional Genomics (SOFG) Towards unified
ontologies for describing biology and
biomedicine 17 20 November 2002 Hinxton Hall
Conference Centre Hinxton, Cambridge,
UK www.wellcome.ac.uk/hinxton/sofg