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