Transcript 2006-03_pombe-workshop_AmiGO_jlomax

An introduction to using the
AmiGO Gene Ontology tool
• Gene Ontology (GO) HTML based
application
• Used to browse, query and visualise GO
data
• Can be installed locally
– freely available from GO website
• GO to the geneDB S. pombe web page:
http://www.genedb.org/genedb/pombe/index.jsp
• click ‘AmiGO’
browsable GO
tree
number of genes
annotated to term (+
child terms)
search functions
functions for filtering what
data is displayed in AmiGO
- currently only S.pombe
data is being shown
the tree can be
expanded to show
‘child’ terms by clicking
on the + symbol before
the term
‘child’ terms
of biological
process
expanded node, can be
closed again by clicking
the - icon
number of genes annotated
to term, and its children
node ‘physiological
process’ also open
indicates that a term
has no children
number of genes annotated
to term, and its children
indicates
relationship of term
to its parent. P =
part_of, I = is_a
number of genes annotated
to term, and its children
Searching
• To find a specific term, it’s easiest to
use the search facility in the top left of
the screen
Searching
tick this box to
search for only
exactly matching
strings
select to search for
GO terms
select to search for
annotated genes
search with extra
options e.g. search
only term names
Searching
enter search string
here and click
‘Submit Query’
GO terms
matching
search string
GO term
numerical
identifier
which of the three GO
ontologies the term
belongs to. P = biological
process, F = molcular
function and C = cellular
component
text definition for
the term
clicking on the tree
icon takes you to the
GO tree expanded at
the term
view shows two
different paths
up the tree for
term ‘1,3-betaglucan synthase
activity’
clicking a term
name takes you
to a detailed
view of that
term
term details
all parent terms
of term
links between
term and objects
in other
databases e.g EC
numbers
(scroll down window)
genes annotated to term,
with annotation information
number of genes
annotated to term
gene symbol/name. Links to
page showing all annotations
to gene
gene description
source of annotation i.e. the
database that created the
annotation
links to gene page in S.
pombe database
evidence for annotation mouseover for full name
reference for annotation e.g. PubMed id for paper
filters for setting which data
displayed.
selecting ‘All’ then clicking
‘Submit Query’ will show genes for
all datasources annotated to term
now 31 results
genes from all
databases annotated
to term
(more)
re-set to show only S. pombe data
by selecting from the list, and
clicking ‘Submit Query’
only S. pombe data now
shown again. Filters stay set
within a session.
Searching for genes
enter gene to search
for here, check the
Gene Symbol/Name
box and click
‘Submit Query’
gene matching
search string
other GO
annotations for
gene
click AmiGO icon to
return to main tree
page
open nodes ‘biological process’ -> cellular
process’ ->cellular physiological process
creates a pie-chart showing the distribution of
genes annotated to terms in ‘cellular
physiological process’ node
• QuickGO is another GO browser,
developed at EBI:
http://www.ebi.ac.uk/ego/
• GO terms only does not display
annotations
– can search on UniProt protein ids
select the field to search
on e.g. GO id, UniProt
identifier. Seaches
name/synonym by defaut
select ontology, i.e. biological
process, molecular function,
cellular component, to search.
Seaches all by default.
enter search string and
click ‘Search GO’
matches to search string
click term name to select
term details
(scroll down window)
alternative paths
through tree
view of term
location in tree
compare to different view of same
information in AmiGO