Microarray GO Browser User’s Guide

The Gene Ontology Browser tool provides a means of analyzing microarray data. Given a list of “interesting” spots on an array, it ties the gene functions to their biological roots in a human interpretable form. Selecting tree nodes causes their gene ontology to be mapped back to associated genes, each of which are displayed in a list by corresponding gene symbol and name. List items function as hyperlinks for web browser viewing of their LocusLink information at the NCBI.

User Interface

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The Gene Ontology Browser (as displayed below) is an MDI-style Java application. This style is similar to applications like Microsoft Word, allowing multiple documents to be in use simultaneously. Open documents are listed in the Window pulldown menu with a checkmark preceding the active (selected) document.

Each document contains a tree view of experiment results from microarray data. Opening a document creates a new window with the title of the document displayed in the title bar and any remarks displayed in the Description panel. The Experiment Terms panel displays a hierarchial view of gene ontology terms associated with the experiment results. Each term is displayed preceded (in brackets) by its cumulative and pure frequencies. Selecting one or more terms from the tree will cause the associated Locus ids to be looked up and their symbol/name to be displayed in the scrolled list in the Associated Genes panel. Double-clicking on items in the scrolled list will launch a web browser which will display the item’s LocusLink information. Tool tips display the accession ids for both Gene Ontology terms and LocusLink symbols.

Gene Ontology Browser

Menus

File Pulldown Menu

The File pulldown menu contains all the generic file handling options.

• New...: Creates new Experiment Results data file.
• Open...: Opens an existing Experiment Results data file.
• Close: Closes the current Experiment Results window.
• Export.: Exports data associated with selected nodes of Experiment Results tree hierarchy. Not implmented yet.
• Print.: Prints the Experiment Results tree hierarchy. Currently disabled.
• Quit: Quits the application.

Appearance Pulldown Menu

The Appearance pulldown menu contains the appearance modification options. It allows changing the look and feel of the application via pullright menu selections.

• Look&Feel: Sets the look and feel of the application to be platform-dependent. Menu choices will vary depending on where the application is run. Metal, the cross-platform look and feel, is the default setting.
• Theme: Sets the theme used by the Metal Look&Feel. Themes allow control of many attributes of this look and feel, including colors and fonts.

Window Pulldown Menu

The Window pulldown menu contains all the generic window handling options and an open document list.

• Cascade: Stacks all document windows in a cascade.
• Tile Horizontal: Stacks all document windows from left to right.
• Tile Vertical: Stacks all document windows from top to bottom.
• Document(s): A dynamic list of all open document windows. A checked box is displayed beside the selected (frontmost) document.

Help Pulldown Menu

The Help pulldown menu contains all the options providing basic assistance in using the application.

• Overview: Provides a high level description of the application’s purpose.
• User Guide: Displays this document via web browser.
• About: Provides information about the application itself.

Input/Output

• Environment variables:
  • GOHOME: Root directory of the installation. Mandatory.
  • GODATA: Alternative directory where experiment results data files exist. Defaults to *\$GOHOME/data* directory if unset.
  • GOIMPORT: Alternative directory from where ASCII files containing Locus ids are imported. Defaults to \$GODATA directory if unset.

• Files:
  • go.xml: XML file that contains gene ontology data.
  • <datafile>.xml: XML file that contains experiment results data.
  • <datafile>.txt: ASCII file that contains Locus ids, one per line, that can be imported to create an experiment results data file.

• Command line activation:
  java
  • Dgobrowser.home=pathname Specifies same thing as \$GOHOME
  • Dgobrowser.data=pathname Specifies same thing as \$GODATA
  • Dgobrowser.import=pathname Specifies same thing as \$GOIMPORT
  • Djava.rmi.server.hostname=localhost Specifies symbolic name of host where RMI registry is running
  • Djava.security.policy=java/policy/GOBrowser.policy Specifies the Java security policy file
  • jar java/jars/GOBrowser.jar Specifies the GUI application archive
    [filename] Specifies an XML data file to open on startup