Browsing and searching the Gene Ontology

GO Browsers

This will display the gene ontology graph with the three ontologies; biological process, cellular component and molecular function:

• First of all, each term gets one horizontal line. The first thing on each line can be either a , or a icon. can be used to expand a node, showing all the children of the selected term:

  

• can be used to deselect a term, closing the node. Finally, means that the term on that line has no children.
• The next thing on each line can be either a or icon. They represent, respectively, a part_of or is_a relationship.
• The next part of each line is the go id and name of that term seperated by a colon. This can be clicked to get a more detailed view of that term, including all genes and gene products annotated to the term:

  

• Following this is a number in parentheses. This tells the total number of gene associations which have been annotated to this term or to a more specific term below this in the GO tree. Note that this number does not include genes which have been electronically annotated (Evidence code IEA). This is due to the large numbers of these annotations as well as the fact that they may be of lower quality.

• Terms may be followed by the icon. Clicking this icon will bring you to a pie chart which displays the percentage of gene products annotated to each term below the selected one:

  

  The final thing to note is that selected terms in each graph are bold.

   Open the node 'biological process', then
  open 'cell growth and/or maintenance', then 'cell proliferation'
  

  Q. How many of the children of 'cell proliferation' have no children of their own?

  Q. How many annotations (non-IEA) does 'cell proliferation' have to it?

  Q. What relationship does 'regulation of cell proliferation' have to its parent 'cell proliferation'?

  
  

  Multiple Parentage

  Perform an exact search (tick the 'exact' button next to the search box) for 
  the GO term 'DNA replication', then click on it.
  

  You will be presented with a window showing a detailed view of this term:

  

  At the top is the term name, any synonyms of the term and the term's definition. Next is the lineage of the term, showing the term with all of its parents but no children. Note that this particular term has multiple paths of parentage.

  QuickGO

  Another good way to view this is by using the European Bioinformatics Institute QuickGO Browser:

  

  

  Q. How many different direct parents (i.e. only one generation away) does 'DNA replication' have?

  Returning to AmiGO again, following this is a list of External Database References, i.e. links to representations of this term in other databases. For more info on the contributing databases see the main Gene Ontology page:

  Finally there is a list of all gene associations: The column headings are fairly self-explanatory. The second column tells which database that gene association is from (i.e. Flybase). The next column has a list of all of the evidence for that gene association. Many of these will have the type of evidence, i.e. GO Evidence Code, linked to that reference in an external database. To get desciptions of the different evidence codes, click the link on the 'Evidence' column header.

  Note that the associated gene product list has a selector for filtering gene products of interest. You can choose which databases you'd like to pull gene products from, which evidence codes you'd like to see and then submit the query to get an updated list.

  

    Change the view so that gene associations with all evidence codes are displayed.  
  
  

  Q. The associated gene 'cutlet' is from which database, on the basis of which evidence code?

  Q. What is the difference between the IEA and NAS evidence codes?

  
  

  Querying

    Shut the popup window and return to the main page.  
  
  

  On the right side of the Navigation bar at the top of the page on the screen, there is a form to query the Gene Ontology graph. Either GO terms or GO associated gene products can be searched by checking the 'terms' or 'gene products' boxes respectively.

    Perform a search for gene products containing the text 'wall'
  
  

  

  The results list displays all gene products containing the text 'wall', the gene product symbol, the name of that external database which the gene product is from, all GO terms to which the product has been associated and the types of evidence linking the gene product to that term.

  Q. How many GO terms is the TAIR gene product 'WAK1' associated with?

  If you'd like more search options, you can click on the 'Advanced Queries' link. This box lets you choose which fields you'd like to search for either query.

  

   Perform a
  search for GO terms with the text 'endoplasmic reticulum' in their name
  or definition.
   

  Each row of the results table contains one GO term. Clicking the name of that term will bring you to the detailed view. Clicking the link to "Tree view" will replace your list of hits with the term selected in the browsing view where you can expand nodes to explore that terms parents, siblings and children. The last column has the definition of term, if there is one.

  Q. How many gene products are annotated to the term 'endoplasmic reticulum receptor'?

  
  

  Pie Charts

    Select the term 'biological process' and click the pie icon at the end of the line.
  

  Q. What term makes up the biggest slice of the 'biological process' annotations?

  Q. What makes up the biggest slice of the biggest slice (and so on!)?

  
  

  GOst

  GOst is the Gene Ontology Blast server - it allows you to Blast a protein sequence against all gene products that have a GO annotation.

  

  
  Return to the main AmiGO page and click 'GOst search' (under the submit button). 

  This is an example of the result of a Gost search.

  

  Q. Try searching for your favourite gene product.

  Q. Does this gene product already have a GO association?

  Other GO Browsers

  There are many other tools that you can use to access GO and the majority of these are listed on the GO Tools page.

   

  last modified October-2003	Report problems with this website to webmaster@geneontology.org
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