2009-02_johninnesroadshow_go_jdeegan.ppt

13. April 2023

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_...


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.

http://www.kilbot.com.au/wp-content/shop/careful-scientist.gifhttp://www.teamtechnology.co.uk/f-scientist.jpg

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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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attacked

time

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



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


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



See which processes are upregulated or downregulated.


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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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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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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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attacked

time

control

Puparial adhesionMolting cyclehemocyanin

Immune responseToll regulated genes

Amino acid catabolismLipid metobolism

Peptidase activityProtein catabloismImmune response




…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

Reactome

E. Coli hub

2009-02_johninnesroadshow_go_jdeegan.ppt

Documents

gene ontology work

gene ontology project

p05147 pmid

favourite gene product

car ontology

ida p05147

ida pmid

department of biology