Overview of Java TreeView


What Does it Do?

Java TreeView renders gene expression data into several interactive views. The main treeview application considers these views interchangeable, and it is possible to define additional views. This capability will be exploited to speed development of new programs; treeview itself is tried and true, and should not be touched in my opinion.


Gene expression data is organized into rows and columns, where the rows correspond to genes, and the columns correspond to experiments. Thus, the value in row m, column n, is a measure of the expression of gene m in experiment n. The value used is commonly the log2 of the ratio of the experimental sample to the control. These values are rendered in a red-green color scale, where red represents higher expression and green indicates lower expression in the given experiment.


Clicking on the global view, or clicking and dragging, will cause a zoomed version of the global view to appear in the zoom view pane.

GTRView, ATRView

If the data has been hierarchically clustered using SMD, gene trees and array trees can be displayed. The trees represent the degree of correlation between nodes. For example, in the array tree case, similar arrays are joined together at each step until eventually there are only two clusters of genes which are joined at the top of the view to form a single root for the tree.

TextView, ArrayNameView

The available annotation for genes and arrays is rendered adjacent to the ZoomView. The annotation is taken from a column of the .cdt file, which is a tab-delimited text file which can be edited in Excel.