2009-02_JohnInnesRoadshow_GO_jdeegan.ppt

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EBI is an Outstation of the European Molecular Biology Laboratory.

The Gene Ontology Project

An Introduction

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There is a lotof biological research output.

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Search on mesodermdevelopment…

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You get 6752results!

How will you ever find whatyou want?

Anotherexample…

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Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

attacked

time

controlSelected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

Microarray datashows changed expression ofthousands of genes.

How will you spot the patterns?

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Scientists work hard.

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There are lots of papers to read.

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more everyweek.

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andmore…

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more andmoreand more!

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Help!Help!Help!Help!more and

moreand more!

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Ontology is a way to capture knowledge in a written and computable form.

Computable means that the computer finds patterns so we don’t have to.

ComputableComputable

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Ebay search (keyword ‘lead’)

v. Pubmed search (keyword ‘flower’)

Demo and practical work

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The Gene Ontology

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This is ourbrowser.

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Search onmesoderm development.

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Here is mesoderm development.

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Definition of mesodermdevelopment.

Gene productsinvolved in mesodermdevelopment.

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There are many gene products involved in mesoderm development.

You can read papers describingwhat is knownabout them.

But fewer gene products than papers.

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Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

attacked

time

controlSelected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

13. April 202322Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

attacked

time

control

Puparial adhesionMolting cyclehemocyanin

Defense responseImmune responseResponse to stimulusToll regulated genesJAK-STAT regulated genes

Immune responseToll regulated genes

Amino acid catabolismLipid metobolism

Peptidase activityProtein catabloismImmune response

Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

See which processes are upregulated or downregulated.

Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

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Practical work: Search AmiGO

Did you find your favouritegene product or process?

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How does theGene Ontology work?

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The Gene Ontologyis like a dictionary

term: transcription initiation

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.

id: GO:0006352

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Clark et al., 2005

part_of

is_a

The whole system.

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Mitochondrial P450 (CC24 PR01238; MITP450CC24)

An example…

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GO cellular component term:GO:0005743

Where is it?

Mitochondrial p450

mitochondrial inner membrane

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GO molecular function term:GO:0004497

What does it do?

substrate + O2 = CO2 +H20 product

monooxygenase activity

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http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html

GO biological process term: GO:0006118

Which process is this?

electron transport

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Clark et al., 2005

part_of

is_a

The whole system.

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The Gene Ontology is for all species

and that meanswe have to

*bridge*

some language barriers.

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http://www.darknessandlight.co.uk/cambridge_photographs.html

http://www.lockeheemstra.com/italy/bridge-of-sighs-venice.html

Ponte dei Sospiri,Venice.

Bridge of Sighs,Cambridge.

Same name, same thing?

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TactitionTactile sense

Taction

?In biology…

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Tactition Tactile senseTaction

perception of touch ; GO:0050975

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Bud initiation?

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= tooth bud initiation

= reproductive bud initiation

= branch bud initiation

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Demo: Writing an ontology

The car ontology

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• Demo: The gene ontology

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Categorization of gene productsusing GO is called annotation.

So how does that happen?

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P05147

Choose your favourite gene.

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P05147

PMID: 2976880

Find a paperabout it.

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P05147PMID: 2976880

GO:0047519

Find the GO term describing itsfunction, process or location of action.

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P05147

PMID: 2976880

IDA

GO:0047519

What evidencedo theyshow?

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P05147

PMID: 2976880

GO:0047519

IDA

P05147 GO:0047519 IDA PMID:2976880

Write these down…

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Send to the GO Consortium .

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Finding annotations in a paper

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…

Process: response to wounding GO:0009611

wound response

serine/threonine kinase activity,

Function: protein serine/threonine kinase activity GO:0004674

integral membrane protein

Component: integral to plasma membrane GO:0005887

…for B. napus PERK1 protein (Q9ARH1)

PubMed ID: 12374299

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EBI is an Outstation of the European Molecular Biology Laboratory.

Annotation details

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Where to get annotations?

• Non-redundant species database• Contains all GO annotations for given species + other

information.• http://www.arabidopsis.org/

• Multispecies database - GOA• Contains all GO annotations.• http://beta.uniprot.org/

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Evidence codes

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IDA - inferred from direct assay

Enzyme assaysIn vitro reconstitution (e.g. transcription)Immunofluorescence (for cellular component)Cell fractionation (for cellular component)Physical interaction/binding

IEP - inferred from expression pattern

Transcript levels (e.g. Northerns, microarray data)Protein levels (e.g. Western blots)

IGC - inferred from genomic context

Operon structureSyntenic regionsPathway analysisGenome-scale analysis of processes

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IGI - inferred from genetic interaction

"Traditional" genetic interactions such as suppressors, synthetic lethals, etc.Functional complementationRescue experimentsInference about one gene drawn from the phenotype of a mutation in a different gene.

IMP - inferred from mutant phenotype

Any gene mutation/knockoutOverexpression/ectopic expression of wild-type or mutant genesAnti-sense experimentsRNAi experimentsSpecific protein inhibitorsPolymorphism or allelic variation

IPI - inferred from physical interaction

2-hybrid interactionsCo-purificationCo-immunoprecipitationIon/protein binding experiments

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ISS - inferred from sequence or structural similarity

Sequence similarity (homologue of/most closely related to)Recognized domainsStructural similaritySouthern blotting

RCA - inferred from reviewed computational analysis

Large-scale protein-protein interaction experimentsMicroarray experimentsIntegration of large-scale datasets of several typesText-based computation

IEA - Inferred from Electronic Annotation

NAS - non-traceable author statement

ND - no biological data available

TAS - traceable author statement

NR - not recorded

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PMID: 15960829

Should we trust electronic annotations?

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http://www.geneontology.org/GO.indices.shtml

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!version: $Revision: 1.67 $

!date: $Date: 2008/01/21 11:29:01 $

!Mapping of GO function_ontology "enzymes" to Enzyme Commission Numbers.

!original mapping by Michael Ashburner, Cambridge.

!This version parsed from function.ontology on 2008/01/15 14:01:16

!by Daniel Barrell, EBI, Hinxton

!

EC:1 > GO:oxidoreductase activity ; GO:0016491

EC:1.1 > GO:oxidoreductase activity, acting on CH-OH group of donors ; GO:0016614

EC:1.1.1 > GO:oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ; GO:0016616

EC:1.1.1.1 > GO:alcohol dehydrogenase activity ; GO:0004022

EC:1.1.1.10 > GO:L-xylulose reductase activity ; GO:0050038

EC:1.1.1.100 > GO:3-oxoacyl-[acyl-carrier-protein] reductase activity ; GO:0004316

EC:1.1.1.101 > GO:acylglycerone-phosphate reductase activity ; GO:0000140

EC:1.1.1.102 > GO:3-dehydrosphinganine reductase activity ; GO:0047560

EC:1.1.1.103 > GO:L-threonine 3-dehydrogenase activity ; GO:0008743

EC:1.1.1.104 > GO:4-oxoproline reductase activity ; GO:0016617

ec2go mapping

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interpro2go mapping

!date: 2008/01/15 13:01:24!Mapping of InterPro entries to GO!Nicola Mulder, Hinxton!InterPro:IPR000003 Retinoid X receptor > GO:DNA binding ; GO:0003677InterPro:IPR000003 Retinoid X receptor > GO:steroid binding ; GO:0005496InterPro:IPR000003 Retinoid X receptor > GO:regulation of transcription, DNA-dependent ; GO:0006355InterPro:IPR000003 Retinoid X receptor > GO:nucleus ; GO:0005634InterPro:IPR000005 Helix-turn-helix, AraC type > GO:transcription factor activity ; GO:0003700InterPro:IPR000005 Helix-turn-helix, AraC type > GO:intracellular ; GO:0005622InterPro:IPR000006 Metallothionein, vertebrate > GO:metal ion binding ; GO:0046872InterPro:IPR000013 Peptidase M7, snapalysin > GO:extracellular region ; GO:0005576InterPro:IPR000014 PAS > GO:signal transducer activity ; GO:0004871InterPro:IPR000015 Fimbrial biogenesis outer membrane usher protein > GO:transporter activity ; GO:0005215InterPro:IPR000018 P2Y4 purinoceptor > GO:purinergic nucleotide receptor activity, G-protein coupled ; GO:0045028InterPro:IPR000020 Anaphylatoxin/fibulin > GO:extracellular region ; GO:0005576InterPro:IPR000021 Hok/gef cell toxic protein > GO:membrane ; GO:0016020InterPro:IPR000022 Carboxyl transferase > GO:ligase activity ; GO:0016874InterPro:IPR000023 Phosphofructokinase > GO:6-phosphofructokinase activity ; GO:0003872InterPro:IPR000025 Melatonin receptor > GO:integral to membrane ; GO:0016021InterPro:IPR000026 Guanine-specific ribonuclease N1 and T1 > GO:endoribonuclease activity ; GO:0004521InterPro:IPR000028 Chloroperoxidase > GO:peroxidase activity ; GO:0004601

InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

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Manual annotation appears in AmiGO.

Manual and electronic annotationappears in QuickGO.

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Clark et al., 2005

Many species groups annotate.

We see the research of one function across all species.

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Exercise: Search for your favourite gene

and see if the annotation is electronic or manual.

http://www.ebi.ac.uk/ego/

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Submit new GO terms:

http://www.geneontology.org/

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EBI is an Outstation of the European Molecular Biology Laboratory.

GO slims

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Clark et al., 2005

part_of

is_a

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Clark et al., 2005

part_of

is_a

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Whole genome analysis(J. D. Munkvold et al., 2004)

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Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

attacked

time

control

Puparial adhesionMolting cyclehemocyanin

Immune responseToll regulated genes

Amino acid catabolismLipid metobolism

Peptidase activityProtein catabloismImmune response

Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

…analysis of high-throughput data according to GO

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Making Slims:

OBO-Edit

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Reapplying slimmed ontology to annotations:

AmiGO

http://amigo.geneontology.org/

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Converting IDs:PICR

http://www.ebi.ac.uk/Tools/picr/

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GOOSEhttp://www.berkeleybop.org/goose

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2006 Consortium Meeting,

St. Croix,

U.S. Virgin Islands, March 30 - April 3, 2006

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http://www.geneontology.org

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