Download Presentation - European Bioinformatics Institute

Introduction to the Gene Ontology and GO
Annotation Resources
EBI Bioinformatics Roadshow
15 March 2011
Düsseldorf, Germany
Rebecca Foulger
EBI is an Outstation of the European Molecular Biology Laboratory.
OUTLINE OF TUTORIAL:
PART I: Ontologies and the Gene
Ontology (GO)
PART II: GO Annotations
How to access GO annotations
How scientists use GO annotations
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
PART I: Gene Ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What’s in a name...?
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Q: What is a cell?
A: It really depends
who you ask!
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Different things
can be described
by the same
name
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The same thing can be described by different
names:
•
•
•
•
•
Glucose synthesis
Glucose biosynthesis
Glucose formation
Glucose anabolism
Gluconeogenesis
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Inconsistency in naming of biological concepts
• Same name for different concepts
• Different names for the same concept
 Comparison is difficult – in particular across
species or across databases
Just one reason why the Gene Ontology (GO) is
is needed…
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Why do we need GO?
• Inconsistency in naming of biological
concepts
• Large datasets need to be interpreted quickly
•Increasing amounts of biological data
available
• Increasing amounts of biological data to
come
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Increasing amounts of biological data
available
Search on mesoderm
development…. you get
9441 results!
Expansion of sequence
information
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
1700s
1606
What is an ontology?
• Dictionary:
• A branch of metaphysics concerned with the nature and relations
of being (philosophy)
• A formal representation of the knowledge by a set of concepts
within a domain and the relationships between those concepts
(computer science)
• Barry Smith:
• The science of what is, of the kinds and structures of objects,
properties, events, processes and relations in every area of
reality.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What is an ontology?
• More usefully:
• An ontology is the representation of something we know about.
“Ontologies" consist of a representation of things, that are detectable or
directly observable, and the relationships between those things.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What is an ontology?
• An ontology is more than just a list of terms (a
controlled vocabulary)
• A vocabulary of terms
• Definitions for those terms
• *** Defined logical relationships between the terms ***
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What’s in an Ontology?
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
What is the Gene Ontology (GO)?
A way to capture
biological knowledge in a
written and computable
form
Describes attributes of
gene products (RNA and
protein)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The scope of GO
What information might we want to capture about a
gene product?
• What does the gene product do?
• Where does it act?
• How does it act?
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Biological Process
what does a gene product do?
A commonly recognised series of events
transcription
cell division
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Cellular Component
where is a gene product located?
• plasma
membrane
• mitochondrion
• mitochondrial membrane
• mitochondrial matrix
• mitochondrial lumen
• ribosome
• large ribosomal subunit
• small ribosomal subunit
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Molecular Function
how does a gene product act?
•
•
insulin binding
•
insulin receptor activity
glucose-6-phosphate isomerase activity
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Three separate ontologies or one large one?
• GO was originally three completely independent
hierarchies, with no relationships between them
• As of 2009, GO have started making relationships
between biological process and molecular function in the
live ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Process
Function
Function
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
• GO IS:
• species independent
• covers normal processes
• GO is NOT:
• NO pathological/disease processes
• NO experimental conditions
• NO evolutionary relationships
• NO gene products
• NOT a nomenclature system
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Aims of the GO project
• Compile the ontologies
• Annotate gene products using ontology terms
• Provide a public resource of data and tools
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Anatomy of a GO term
Unique identifier
Term name
Definition
Synonyms
Crossreferences
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Ontology structure
•
GO is structured as a hierarchical directed acyclic graph
(DAG)
•
Terms can have more than one parent and zero, one or
more children
•
Terms are linked by relationships, which add to the
meaning of the term
node
• Nodes = terms in the ontology
edge
node
• Edges = relationships between
the concepts
node
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Relationships between GO terms
• is_a
• part_of
• regulates
• positively regulates
• negatively regulates
• has_part
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
is_a
• If A is a B, then A is a subtype of B
• mitotic cell cycle is a cell cycle
• lyase activity is a catalytic activity.
• Transitive relationship: can infer up the graph
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
part_of
• Necessarily part of
• Wherever B exists, it is as part of A. But not all B is part of A.
A
B
• Transitive relationship (can infer up the graph)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
regulates
• One process directly affects another process or quality
• Necessarily regulates: if both A and B are present, B always regulates
A, but A may not always be regulated by B
A
B
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
has_part
• Relationships are upside down compared to is_a and part_of
• Necessarily has part
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
is_a complete
• For all terms in the ontology, you have to be able to reach
the root through a complete path of is_a relationships:
• we call this being is_a complete
• important for reasoning over the ontology, and ontology development
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
True path rule
• Child terms inherit the meaning of all their parent terms.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How is GO maintained?
• GO editors and annotators work with experts to remodel specific
areas of the ontology
• Signaling
• Kidney development
• Transcription
• Pathogenesis
• Cell cycle
• Deal with requests from the community
• database curators, researchers, software developers
• Some simple requests can be dealt with automatically
• GO Consortium meetings for large changes
• Mailing lists, conference calls, content workshops
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Requesting changes to the ontology
• Public Source Forge (SF) tracker for term related issues
https://sourceforge.net/projects/geneontology/
Why modify the GO?
• GO reflects current knowledge of biology
• Information from new organisms can make existing terms
and arrangements incorrect
• Not everything perfect from the outset
• Improving definitions
• Adding in synonyms and extra relationships
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Ensuring Stability in a Dynamic Ontology
•
Terms become obsolete when they are removed or redefined
•
GO IDs are never deleted
•
For each term, a comment is added to explain why the term is
now obsolete
•
Alternative GO terms are suggested to replace an obsoleted
term
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Searching for GO terms
http://www.ebi.ac.uk/QuickGO/
http://amigo.geneontology.org
… there are more browsers available on the GO Tools page:
http://www.geneontology.org/GO.tools.browsers.shtml
The latest OBO Gene Ontology file can be downloaded from:
http://www.geneontology.org/ontology/gene_ontology.obo
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Browsing the Gene Ontology using
QuickGO
• Exercise 1
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
PART II: GO Annotation
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
E. Coli
hub
http://www.geneontology.org
Reactome
A GO annotation is…
A statement that a gene product:
1.
has a particular molecular function
Or is involved in a particular biological process
Or is located within a certain cellular component
2.
as determined by a particular method
3.
as described in a particular reference
Accessio
n
Nam
e
GO ID
GO term name
Reference
Evidence Code
P00505
GOT2
GO:0004069
Aspartate transaminase
activity
PMID:2731362
IDA
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Evidence codes
http://www.geneontology.org/GO.evidence.shtml
IDA: enzyme assay
IPI: e.g. Y2H
BLASTs, orthology
comparison, HMMs
subcategories of ISS
review papers
GO evidence code decision tree
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Gene Ontology Annotation (GOA)
The GOA database at the EBI is:
• The largest open-source contributor of annotations to GO
• Member of the GO Consortium since 2001
• Provides annotation for 321,998 species (February 2011 release)
• GOA’s priority is to annotate the human proteome
• GOA is responsible for human, chicken and bovine annotations in the
GO consortium
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GOA makes annotations using two methods
• Electronic

• Quick way of producing large numbers of annotations
• Annotations are less detailed
• Manual 
• Time-consuming process producing lower numbers of
annotations
• Annotations are very detailed and accurate
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Electronic annotation by GOA
• 1. Mapping of external concepts to GO terms
•
InterPro2GO (protein domains)
•
SPKW2GO (UniProt/Swiss-Prot keywords)
•
HAMAP2GO (Microbial protein annotation)
•
EC2GO (Enzyme Commission numbers)
•
SPSL2GO (Swiss-Prot subcellular locations)
• 2. Automatic transfer of annotations to orthologs
Ensembl compara
Macaque
Chimpanzee
Cow
Guinea Pig
Dog
Rat
Mouse
Chicken
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Mappings of concepts from UniProtKB files
Aspartate transaminase activity ; GO:0004069
lipid transport; GO:006869
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Automatic transfer of annotations to
orthologs
Human
Mouse
Rat
Zebrafish
Xenopus
Ensembl COMPARA
• Homologies between different species calculated
Currently provides
479,961 GO annotations for
• GO terms projected from MANUAL annotation only (IDA, IEP, IGI, IMP, IPI)
60,515 proteins •from
49orthologies
speciesused.
(February 2011 release)
One-to-one
Macaque
Chimpanzee
Xenopus
Human
Guinea Pig
Rat
Human
Mouse
Tetraodon
Rat
Cow
Dog
Chicken
Mouse
Fugu
Zebrafish
Manual annotation by GOA
• High-quality, specific annotations using:
• Peer-reviewed papers
• A range of evidence codes to categorize the types of evidence
found in a paper
www.ebi.ac.uk/GOA
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Finding annotations in a paper
…for B. napus PERK1 protein (Q9ARH1)
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
serine/threonine kinase
, In addition, the
PERK1 has serine/threonine
kinaseactivity
activity,
location of a PERK1-GTP fusion protein to the plasma
membrane supports the prediction that PERK1 is an
integral membrane
integral
membraneprotein
protein…these kinases have been
implicated in early stages of wound
woundresponse…
response PubMed ID: 12374299
Function:
protein serine/threonine kinase activity
GO:0004674
Component:
integral to plasma membrane
GO:0005887
Process:
response to wounding
GO:0009611
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Additional information
• Qualifiers
Modify the interpretation of an annotation
•
•
•
NOT (protein is not associated with the GO term)
colocalizes_with (protein associates with complex but is not a bona fide member)
contributes_to (describes action of a complex of proteins)
• 'With' column
Can include further information on the
method being referenced
e.g. the protein accession of an interacting protein
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The NOT qualifier
• NOT is used to make an explicit note that the gene
product is not associated with the GO term
• Also used to document conflicting claims in the literature
• NOT can be used with ALL three gene ontologies
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
In these cells, SIPP1 was mainly present in the
nucleus, where it displayed a non-uniform,
speckled distribution and appeared to be
excludedfrom
from
the
nucleoli
excluded
the
nucleoli.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The colocalizes_with qualifier
Gene products that
are transiently or
peripherally
associated with an
organelle or complex
ONLY used with GO component ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Immunoblot analysis with anti-PSI polyclonal
antibodies of U1 snRNP particles affinity purified from
Drosophila embryonic nuclear extracts showed that
PSI
PSI is
is physically
physicallyassociated
associatedwith
withU1
U1snRNP
snRNP(Figure
1A, top panel).
Associationof
ofU1
U1snRNP
snRNPwith
with GST-PSI
GST-PSI was detected
Association
by ethidium bromide staining of the selected snRNAs
and was confirmed by blot hybridization with an
antisense U1 snRNA riboprobe (Figure 1C, lane 4).
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
The contributes_to qualifier
• Where an individual gene product that is part of a complex can be
annotated to terms that describe the action (function or process) of
the whole complex
• contributes_to is not needed to annotate a catalytic subunit.
Furthermore, contributes_to may be used for any non-catalytic
subunit, whether the subunit is essential for the activity of the
complex or not
• Annotations to contributes_to often use the IC evidence code, but
others may also be used.
ONLY used with GO function ontology
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
..we next examined whether a complex
of four proteins can be formed…. As
shown in Figure 4, FLAG-tagged PIG-C
was precipitated efficiently with antiFLAG beads in four combinations with
other proteins (Figure 4A, lanes 1–4)…..
These results strongly suggest that all
four proteins form a complex.
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
whether the
the protein
.. To test whether
proteincomplex
complex consisting of PIG-A,
has
GlcNAc transferase
transferase activity
PIG-H, PIG-C and hGPI1 has
GlcNAc
activity
in vitro….
…incubation of the radiolabeled donor of GlcNAc, UDP[6-3H]GlcNAc, with lysates of JY5 cells transfected with
resultedininsynthesis
synthesis of GlcNAc-PI
GST-tagged PIG-A resulted
GlcNAc-PIand
and
itssubsequent
subsequent
deacetylation
to glucosa- minyl
Its
deacetylation
to glucosa-minyl
phosphatidylinositol
(GlcN-PI)
phosphatidylinositol
(GlcN-PI)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Unknown v.s. Unannotated
• When there is no existing data to support an
annotation, gene is annotated to the ROOT
(top level) term
• NOT the same as having no annotation at all
• No annotation means that no one has looked yet
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
WITH column
• The with column provides supporting evidence for ISS,
IPI, IGI and IC evidence codes
ISS: the accession of the aligned protein/ortholog
IPI: the accession of the interacting protein
IGI: the accession of the interacting gene
IC: The GO:ID for the inferred_from term
WITH
column
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How to access
GO annotation data
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Where can you find annotations?
UniProtKB
Ensembl
Entrez gene
Gene Association Files
• 17 column files containing all information for each annotation
GO Consortium website
GOA website
GO browsers
QuickGO browser
Search GO terms
or proteins
Find sets of
GO annotations
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Searching for GO annotations
in QuickGO
• Exercise 2
• Exercise 3
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Using QuickGO to create a tailored
set of annotations
• Exercise 4: Filtering
• Exercise 5: Statistics
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How scientists use the GO,
and the tools they use for analysis
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Using GO annotations
• If you wanted to find out the role of a gene product
manually, you’d have to read an awful lot of papers
• But by using GO annotations, this work has already been
done for you!
GO:0006915 : apoptosis
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
How scientists use the GO
•
Access gene product functional information
•
Analyse high-throughput genomic or proteomic datasets
•
Validation of experimental techniques
•
Get a broad overview of a proteome
•
Obtain functional information for novel gene products
•
Some examples…
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
time
Defense response
Immune response
Response to stimulus
Toll regulated genes
JAK-STAT regulated genes
Puparial adhesion
Molting cycle
Hemocyanin
MicroArray data analysis
Amino acid catabolism
Lipid metobolism
Peptidase activity
Protein catabolism
Immune response
Immune response
Toll regulated genes
attackedcontrol
pears
on lw n3d
... lw n3d ...Colored
cted Gene
Tree:
pearson
Coloredby:
by:
: color
Set_LW_n3d_5p_...
Gene
Lis
t:
ch
classification: Set_LW_n3d_5p_...
Gene
List:
Bregje Wertheim at the Centre for Evolutionary Genomics,
Department of Biology, UCL and Eugene Schuster Group, EB
Copy
ofofCopy
of
C5_RMA (Defa...
Copy
of Copy
C5_RMA
(Defa...
genes
allall
genes
(14010)(14010)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Validation of experimental techniques
Rat liver plasma membrane isolation
(Cao et al., Journal of Proteome Research 2006)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Analysis of high-throughput proteomic datasets
Characterisation of proteins interacting with ribosomal protein S19
(Orrù et al., Molecular and Cellular Proteomics 2007)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Obtain functional information for novel
gene products
MPYVSQSQHIDRVRGAIEGRLPAPGNSSRLVSSWQRSYEQYRLDPGSVIGPRVLTS
SELR DVQGKEEAFLRASGQCLARLHDMIRMADYCVMLTDAHGVTIDYRIDRDRRGD
FKHAGLYI GSCWSEREEGTCGIASVLTDLAPITVHKTDHFRAAFTTLTCSASPIFAPTG
ELIGVLDAS AVQSPDNRDSQRLVFQLVRQSAALIEDGYFLNQTAQHWMIFGHASRN
FVEAQPEVLIAFD ECGNIAASNRKAQECIAGLNGPRHVDEIFDTSAVHLHDVARTDTI
MPLRLRATGAVLYAR IRAPLKRVSRSACAVSPSHSGQGTHDAHNDTNLDAISRFLHS
RDSRIARNAEVALRIAGK HLPILILGETGVGKEVFAQALHASGARRAKPFVAVNCGAIP
DSLIESELFGYAPGAFTGA RSRGARGKIAQAHGGTLFLDEIGDMPLNLQTRLLRVLA
EGEVLPLGGDAPVRVDIDVICA THRDLARMVEEGTFREDLYYRLSGATLHMPPLRER
ADILDVVHAVFDEEAQSAGHVLTLD GRLAERLARFSWPGNIRQLRNVLRYACAVCDS
TRVELRHVSPDVAALLAPDEAALRPALA LENDERARIVDALTRHHWRPNAAAEALGM
InterProScan
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Annotating novel sequences
• Can use BLAST queries to find similar sequences with
GO annotation which can be transferred to the new
sequence
• Two tools currently available;
• AmiGO BLAST (from GO Consortium)
http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi
• searches the GO Consortium database
• BLAST2GO (from Babelomics)
http://www.blast2go.org/
• searches the NCBI database
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
AmiGO BLAST
Exportin-T from Pongo abelii (Sumatran
orangutan)
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Numerous Third Party Tools
• Many tools exist that use GO to find common biological
functions from a list of genes:
http://www.geneontology.org/GO.tools.microarray.shtml
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO tools: enrichment analysis
• Most of these tools work in a similar way:
• input a gene list and a subset of ‘interesting’ genes
• tool shows which GO categories have most interesting genes
associated with them i.e. which categories are ‘enriched’ for
interesting genes
• tool provides a statistical measure to determine whether
enrichment is significant
• Try exercise 7 at home
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO slims
• Many GO analysis tools use GO slims to give a broad
overview of the dataset
• GO slims are cut-down versions of the GO and contain a
subset of the terms in the whole GO
• GO slims usually contain less-specialised GO terms
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Slimming the GO using the ‘true path rule’
Many gene products are associated with a
large number of descriptive, leaf GO nodes:
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Slimming the GO using the ‘true path rule’
…however annotations can be mapped up
to a smaller set of parent GO terms:
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
GO slims
• Custom slims are available for download;
http://www.geneontology.org/GO.slims.shtml
• Or you can make your own using;
•
QuickGO
• http://www.ebi.ac.uk/QuickGO
•
AmiGO's GO slimmer
• http://amigo.geneontology.org/cgi-bin/amigo/slimmer
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Slimming with QuickGO
Search GO terms
or proteins
Find sets of
GO annotations
Map-up annotations
with GO slims
www.ebi.ac.uk/QuickGO
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Exercise
Map-up annotation using a GO slim
• Exercise 6
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Just some things to be aware of….
•
The GO is continually changing
• New terms created
ontology
• Existing terms obsoleted
• Re-structured
annotation
• New annotations being created
•
ALWAYS use a current version of ontology and annotations
•
If publishing your analyses, please report the versions/dates you use:
http://www.geneontology.org/GO.cite.shtml
•
Differences in representation of GO terms may be due to biological
phenomenon. But also may be due to annotation-bias or experimental assays
•
Often better to remove the ‘NOT’ annotations before doing any large-scale
analysis, as they can skew the results
GO and GO Annotation, EBI Bioinformatics Roadshow. Düsseldorf. March 2011
Thank you
EBI is an Outstation of the European Molecular Biology Laboratory.