Functional Treeview

 

Functional Treeview

Integrated Display of Functional Annotation with Microarray Data

Vineet Joshi, Johannes Freudenberg, Mario Medvedovic *

Department of Environmental Health,

University of Cincinnati College of Medicine,

3223 Eden Av. ML 56, Cincinnati OH 45267-0056,

* To whom correspondence should be addressed

Abstract

Java Treeview is an open-source and platform-independent tool used for viewing microarray and results of cluster analysis of microarray data. Functional Treeview (FTreeview) extends Java Treeview and adds features to interactively display functional annotation for all cluster nodes of interest. It facilitates integration and mining of the pre-computed functional annotations of gene expression clusters and the clustering structure of gene expression data. Input files for FTreeView can be generated using an independent R-package. When pre-computed functional annotations are not available, FTreeView facilitates functional annotation and enrichment analysis by submitting genes from the selected cluster to the online functional annotation tools of DAVID (Dennis, Jr. et al., Genome Biol. 4: 3, 2003). Availability of all this information in one integrated and interactive display makes FTreeview a unique tool aimed at increasing the ability of researchers to effectively interpret results of their analysis. In addition to the standalone application, we developed the Java webstart version of FTreeView which to be used as the web-application. In this poster we demonstrate the functionality of both versions of FTreeView.

Availability

Functional Treeview can be used in either of the following formats:

  • As a Java Web Start application over the web.
  • As a standalone desktop application.

The Java Web Start application can be used for deploying and demonstrating the results of functional analysis over the web. An example of the same is : This example displays the data set by Miller et al ( Miller et al., PNAS 102(38):13550-5. (2005) ), with gene clustering done using GIMM ( Liu et al., Bioinformatics 22:1737-44. (2006) ).

Java Web Start needed to launch this application is a standard component of the Java runtime available from Sun Microsystems.

We will soon release the stand-alone desktop version of Functional Treeview along with its source code. Watch out this web page for updates!

Contact

mario.medvedovic@uc.edu