Trans-NIH Jak-Stat Initiative

Java TreeView of Test samples for Muscle - Stat5MKO-GH vs WT-GH

Muscle cells from Stat5-null and control 15-week mice without GH treatment. This used mAdb test: EG3.2-test-1-FC-JTV.

Muscle: EG003.2
(T2-)  Stat5MKO-GH vs WT-GH --- fold changes < 2X and p-Value<0.05
It compares two groups of samples as A/B with:
   (A) Samples[Stat5MKO-GH]: EG003.2-04, EG003.2-05, EG003.2-06
   (B) Samples[WT-GH]: EG003.2-01, EG003.2-02, EG003.2-03.

Muscle cells from Stat5-null and control 15-week mice without GH treatment

Click on the button to bring up the Java TreeView hierarchical clustered heat map of the data. Note that you need to have Java enabled and popup windows enabled in your Web browser to use run the Java TreeView applet.

Your browser is ignoring the <APPLET> tag! Look in your navigator bar or preferences to enable Java"

Alternatively, you can download the JTV .zip file to run in the Java TreeView application. The application lets you save the labeled heatmaps in a Postscript, PNG or GIF file and save the state of your examination of the heatmap. You need to install the application separately from the Java TreeView Web site described below.

Java TreeView (JTV) Documentation

Java TreeView is an open-source (jTreeView.sourceforge.net) Java applet that mAdb uses to view heatmaps of gene sets. We also use Java TreeView for looking at data snapshots we have taken of the GSP data. See the discussion on using Java TreeView with Jak-Stat Prospector on the GSP mAdb Java TreeView data.

Java TreeView distribution may be downloaded to run as either a standalone application or Java applet from http://jTreeView.sourceforge.net/.

We have made a slight modification of the applet that is loaded from the Jak-Stat Prospector Web site. The modified applet sets the default web link when you click on a gene probe as the mAdb Feature Report.

The 2004 journal paper by Alok J. Saldanha gives an overview of Java TreeView: "Java Treeview—extensible visualization of microarray data" Bioinformatics 2004 20(17):3246-3248.

There is additional jTreeView documentation on their Web site that includes links to examples, an FAQ, a user guide, Alok J. Saldanha's disertation describing additional aspects of Java Treeview.

NOTE: The Java TreeView applet has been shown to work on Mac OS-X, XP and Win2K.

This Web page was derived in collaboration with GSP consortium members.

Home: jak-stat.nih.gov
Home: Jak-Stat Prospector

Revised: Mon Sep 28 13:56:56 EDT 2009