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

expanded node, can be closed again by clicking the - icon

‘child’ terms of biological process

number of genes annotated to term, and its children

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

Searching

• To find a specific term, it’s easiest to use the search facility in the top left of the screen

Searching

select to search for GO terms

select to search for annotated genes

tick this box to search for only

exactly matching strings

search with extra options e.g. search

only term names

Searchingenter 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-beta-glucan

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

genes annotated to term, with annotation information

(scroll down window)

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 genesenter 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)

view of term location in tree

alternative paths through tree

compare to different view of same information in AmiGO