You get 6752 results! How will you ever find what you want? Another example…
Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI. Microarray data shows changed expression of thousands of genes. How will you spot the patterns? attacked time control
Scientists work hard. http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg
There are lots of papers to read. http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg
more every week. http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg
and more… http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg
more and more and more! http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg
Help! Help! more and more and more! http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg
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. Computable
Ebay search (keyword ‘lead’) v. Pubmed search (keyword ‘flower’) Demo and practical work
The Gene Ontology
This is our browser.
Search on mesoderm development.
Here is mesoderm development.
Definition of mesoderm development. Gene products involved in mesoderm development.
There are many gene products involved in mesoderm development. You can read papers describing what is known about them. But fewer gene products than papers.
attacked time control Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.
attacked time control Puparial adhesion Molting cycle hemocyanin Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Immune response Toll regulated genes Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response See which processes are upregulated or downregulated. Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.
Practical work: Search AmiGO Did you find your favourite gene product or process?
How does the Gene Ontology work?
The Gene Ontology is 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
Clark et al ., 2005 The whole system. part_of is_a
Mitochondrial P450 ( CC24 PR01238 ; MITP450CC24) An example…
GO cellular component term: GO:0005743 Where is it? Mitochondrial p450 mitochondrial inner membrane
GO molecular function term: GO:0004497 What does it do? substrate + O 2 = CO 2 +H 2 0 product monooxygenase activity
http:// ntri.tamuk.edu /cell/ mitochondrion/krebpic.html GO biological process term: GO:0006118 Which process is this? electron transport
Clark et al ., 2005 The whole system. part_of is_a
The Gene Ontology is for all species and that means we have to *bridge* some language barriers.
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?
In biology… Tactition Tactile sense Taction ?
Tactition Tactile sense Taction perception of touch ; GO:0050975
Categorization of gene products using GO is called annotation. So how does that happen?
Choose your favourite gene. P05147
Find a paper about it. P05147 PMID: 2976880
Find the GO term describing its function, process or location of action. P05147 PMID: 2976880 GO:0047519
GO:0047519 What evidence do they show? P05147 PMID: 2976880 IDA
Write these down… P05147 PMID: 2976880 GO:0047519 IDA P05147 GO:0047519 IDA PMID:2976880
Send to the GO Consortium .
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
Where to get annotations?
Non-redundant species database
Contains all GO annotations for given species + other information.
Multispecies database - GOA
Contains all GO annotations.
IDA - inferred from direct assay Enzyme assays In 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 structure Syntenic regions Pathway analysis Genome-scale analysis of processes
IGI - inferred from genetic interaction "Traditional" genetic interactions such as suppressors, synthetic lethals, etc. Functional complementation Rescue experiments Inference about one gene drawn from the phenotype of a mutation in a different gene. IMP - inferred from mutant phenotype Any gene mutation/knockout Overexpression/ectopic expression of wild-type or mutant genes Anti-sense experiments RNAi experiments Specific protein inhibitors Polymorphism or allelic variation IPI - inferred from physical interaction 2-hybrid interactions Co-purification Co-immunoprecipitation Ion/protein binding experiments
ISS - inferred from sequence or structural similarity Sequence similarity (homologue of/most closely related to) Recognized domains Structural similarity Southern blotting RCA - inferred from reviewed computational analysis Large-scale protein-protein interaction experiments Microarray experiments Integration of large-scale datasets of several types Text-based computation IEA - Inferred from Electronic Annotation NAS - non-traceable author statement ND - no biological data available TAS - traceable author statement NR - not recorded
PMID: 15960829 Should we trust electronic annotations?
!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
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.
Manual annotation appears in AmiGO. Manual and electronic annotation appears in QuickGO.
Clark et al ., 2005 Many species groups annotate. We see the research of one function across all species.
Exercise: Search for your favourite gene and see if the annotation is electronic or manual. http://www.ebi.ac.uk/ego/
Submit new GO terms: http://www.geneontology.org/
Clark et al ., 2005 part_of is_a
Clark et al ., 2005 part_of is_a
Whole genome analysis (J. D. Munkvold et al ., 2004)
attacked time control Puparial adhesion Molting cycle hemocyanin Immune response Toll regulated genes Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response 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
Making Slims: OBO-Edit
Reapplying slimmed ontology to annotations: AmiGO http://amigo.geneontology.org/