Overview of Java TreeView
- Open Source, Cross-Platform Gene Expression Visualization Tool
- Interactive Display of Clustered Gene Expression Data, similar to Eisen's TreeView
- Extensible Starting Point for Other Gene Expression Visualization
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
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
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.
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.
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.