Getting Started: The Experiment View

Once GOALIE has terminated the computation of the cluster relationships and their "enrichment", you will be presented with the Experiment View window.

The Experiment View can display a lot of information. Initially, it is presented empty, and by clicking on its elements different views will be displayed.

Let's have an overview of the window. There are three main panels in the window.

• The Clusters Connection view, which is used to display graphical views of clusters and summaries is divided in two sub-panels.
  • The Gannt Chart View shows a summary of the temporal arrangment of up- and down- regulated terms taken from the enrichment of the windoes of clusters and their relations.
  • The Graph View shows a graph of the relations among clusters in different windows.
• The Clusters Information view shows information about the clusters shown in the Graph view. It has several sub-views each showing different bits and pieces of information.
• The Current Selections view shows what terms and items (i.e., genes and/or probes) have been selected by the user for further inspection and refinement of Gantt Chart View.

Gantt Chart View

Let's click on the Show all terms button in the Gantt Chart View (since we do not have any term selected, clicking on Show selected terms would produce an empty view). GOALIE computes a summary of the "profile" of each term across the whole windowed time course.

For each term you see what its overall behavior is in each window (computed as an average of time-course profile of the items tagged with the term as a result of the enrichment procedure). The color coding is the following: red for "up-regulated" terms, green for down-regulated terms, and black terms corresponding to non changing profiles of the underlying support items (i.e., genes, probes, etc.)

In the view above, the term sulfate transport is "up-regulated" in the first cluster window, "down-regulated" in the second cluster window and unchanged in the remaining three windows.

Navigating this window will allow you to have a bird's eye view of the changing "behavior" of the enrichment terms over the time-course.

Graph View

Let's click on the Graph View tab now. After a while, you will get to a view like the following one. Click on any text label, which corresponds to a cluster in one window, to obtain the set of genes/probes that belong to it and the set of term enrichment (GO terms in this case) that go with them.

Most elements in the view are left- and rigth-clickable.

Right clicking in the main graph window pops up the following menu.

Let's select the Maximum Depth: none... menu item and enter 2 in the following input dialog. This will reduce the depth of the DAG starting from the first cluster window.

The result of reducing the depth of the graph view is to display only the first cluster window with the possible connections to clusters in the second window. The Cluster name text and the numbered dot (the Connection) are selectable with the left button. Double-clicking on them with the left button will expand or collapse the "node".

After a few of these operations you may find yourself in a situation like the one shown in the next diplay.

In this view, we have a selected connection and all its information displayed in the various sub-tabs in the Clusters Information panel. The view shows information about the cluster alpha-0-28-cluster-9 as the Source Cluster of the selected connection. The three sub-panels contain the list of genes in the cluster, the Categorization - i.e. the "enrichment" - of the cluster (a tree view with only the most specific terms listed), and a view of which genes support a given enrichment term (Genes by term). The views which contain terms are organized according to schemed commonly used by several "ontology browsers".

Each element in the views is selectable (it will be added to the Current Selections list with visual effects on the main graph view). Right clicking on the elements will pop up a context dependent menu.

Selecting one or the other menu item will pop up a web browser pointing to the selected location. For GO terms, AmiGO will be looked for, while for genes/probes there is a choice to look for the terms either in Entrez or, if accessible, in the Affymetrix site.

The Destination Cluster is symmetric, but it may be empty if no connection is selected.

If a connection is selected, then the Venn view contains a graphical summary - a Venn diagram - of how many genes are shared between the two clusters.

The Cluster plots view is always active and just shows the profiles of the selected clusters.

Selecting a few genes will color some of the connections and of the cluster in the view in green as it is shown in the next view. Note that there is another un-expanded connection to another cluster where one of the selected genes is present. Note also that the centroid of a cluster s also diplayed at this point.

Selecting terms will likewise color some of the connections and of the cluster in the view in red as it is shown in the next view.

When a cluster or a connection comprises both selected genes/probes and selected terms then they are colored in blue as it is shown in the next view.

Selecting the Connection Information panel will show information about the terms that are maintained between the two clusters, terms that belong to only the source cluster and terms that belong only to the destination cluster. This is another view of the "enrichment" results.

Finally, going back to the Gantt Chart view, we can now concentrate only on the selected terms to view their relation with the time course experiment.

In the following we will see how to compare two different experiments.

• Back to Getting Started with GOALIE.
• Forward to Comparing two experiments.