EGAN Tutorial: Interface Basics. October, 2009 Jesse Paquette UCSF Helen Diller Family Comprehensive Cancer Center firstname.lastname@example.org. Preamble. This document has many slides with multi-step animations Best viewed in Slide Show mode The EGAN graphical user interface is evolving
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UCSF Helen Diller Family Comprehensive Cancer Center
Welcome to EGAN!
Here’s the EGAN interface.
There’s a lot of information, so the first thing you’ll want to master is the ability to hide the parts you don’t want to see.
The Network View
The Node Table
The EGAN interface can be divided into three major components.
The Bottom Tables
There is a divider between the Network View and the Node Table. You can drag this divider right and left to provide more room for either the Network View or the Node Table, respectively.
If you wan to completely maximize the Network View, click the Maximize button.
There’s also a divider between the upper section of the interface and the Bottom Tables. You can drag this divider up and down.
There’s a button to hide just the Node Table.
And a button to hide just the Bottom Tables.
When you have experiment results loaded, there are four tables available. To show a table, click the corresponding tab.
Let’s move on to the Bottom Tables.
Right now the Entrez Gene row is selected. Therefore all Entrez Gene nodes are listed in the Node Table.
The first table tab is the Node Types Table. This table lists all the possible node types that can be shown in the Node Table above.
Now all KEGG nodes are visible in the Node Table.
Select the KEGG row in the Node Types Table.
These rows cannot be selected like in the Node Types Table. However, take note of the checkboxes in the first column.
When you click one of these checkboxes, the corresponding edge type will be disabled in EGAN. When disabled, edges of this type will not be shown in the Network View or used for enrichment calculations.
Click the Edges tab to swap to the Edge Types Table.
Now the table displays all the types of gene-gene edges currently available in EGAN.
Click the Expts. tab to swap to the Experiments Table.
Now the table displays all experiment results that have been loaded in EGAN.
These checkboxes will allow you to show/hide some of the experiment columns in the Node Table.
The Heatmap Table is currently under development. When genes are shown in the Network View, they will also be present here as rows in the Heatmap Table.
Let’s move on to the Node Table. Show the Entrez GeneNode Table by clicking the Entrez Gene row in the Node Types Table.
Let’s maximize our view of the Entrez GeneNode Table by dragging the divider to the left.
Now examine the rows and columns in the Node Table. Each row displays information corresponding to an Entrez Gene ID.
There are columns that list pre-collated information about each gene, and columns that display information about that gene in the context of your experiments.
A useful feature of the Node Table is the ability to sort the gene rows by one or more columns.
Click on the p-value Affymetrix column header. The first click will sort the rows in ascending order, a second will sort the rows in descending order. Make sure the rows are sorted in ascending order.
Let’s select all genes that have Affymetrix p-values of 0.0. We’re going to show them on the Network View.
Click on the top gene row (ZKSCAN3) and drag downwards until you have selected all genes with Affymetrix p-values of 0.0.
You should have selected 68 genes. How can you know how many genes are selected? Take a look down in the Node Types Table. The Selected Nodes column should show that there are 68 Entrez Gene nodes selected.
Now we’re going to show these nodes in the Network View. Drag the divider back to the right so you can see the Network View. You can also click the Hide node table button above the Node Table.
Click the Show selected button to show all selected nodes.
Now all 68 selected genes are shown in the Network View…but they’re all located in the same spot! To lay them out automatically, use the Force layout button at the top of the Network View.
Ok, we’re almost done with this tutorial. Just a few quick pointers about using the Network View.
There are lots of helpful buttons and right-click pop-up menus
If you hover the mouse over a button, a tooltip will describe what the button will do
Try right-clicking on rows in the Node Table/Bottom Tables and also on nodes and edges in the Network View.
There’s a lot of functionality in EGAN