Visualization of Functional Links in Tuberculosis with LGL

    This page provides the necessary data and information to visualize the analisys behind the Tuberculosis Protein Network Server in either 2D or 3D.  LGL provides the layout and visualization, while the predictive analisys roots in phylogentic profiles, operon predictions, and rosetta stones. All software can be obtained through the LGL page.

 2D

    The 2D visualization use the 2D coordinates of the layout, a file that describes the edges, and lglview, a JAVA program for visualizing 2D graphs.  This is a .jpg snapshot of part of the 2D visualization using the files provided below. More information on how to use lglview is available through the README. The following files are available here:

2D.coords - The coords of the vertices in 2D space.
edges.lgl - The edges describing the predicted functional links.

While the above two files are the minimum for lglview, additional files provide some insight into the edges:

edge_colors - Each type of predicted interaction is assigned a specific RGB color:
    Operon Prediction: [1 0 0] (Red)
    Phylogenetic Profile Prediction: [0 1 0] (Green)
    Rosetta Stone Prediction: [0 0 1] (Blue)
    Some functional links are predicted by more than one method, in which case the edge is colored [1 1 0] (Yellow).

vertex_colors - Every vertex has the same color, [0 1 1]. This file is not really necessary for the 2D visualization but it is provided.

3D

    Some folks might prefer the 3D visualization. Warning: the VRML files generated from networks of this size are very memory intensive.  This is recommended for Pentium4 or equivalent workstations with 1Gb of memory, and a very good graphics card.

3D.coords - The coords. of the vertices in 3D space.
tb.wrl - The VRML file.  The same color vectors in the 2D visualization are already applied to this file.

    All of the files provided on this page allow you to generate your own colors and notation for the predicted funcional links using the programs available through the LGL page. The visualizations are best used in tandem with the Tuberculosis Protein Network Server.

Copyright © 2002, Edward Marcotte, Shailesh Date, and Alex Adai. This site is not intended for commercial use. The tuberculosis protein network data and server is the property of the Regents of the University of Texas, and cannot be used for commercial purposes without written permission of Edward Marcotte and the Regents of UT. It is forbidden to redistribute, derivatize, or encapsulate the tuberculosis protein network server or data in another database without permission. Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of UT and Edward Marcotte. All copies or mirrors of the tuberculosis protein network server must carry this notice.