Browsing Multidimensional Molecular Networks with the Generic Network Browser (N‐Browse)
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
N?Browse is a graphical network browser for the visualization and navigation of heterogeneous molecular interaction data. N?Browse runs as a Java applet in a Web browser, providing highly dynamic and interactive on?demand access to network data available from a remote server. The N?Browse interface is easy to use and accommodates multiple types of functional linkages with associated information, allowing the exploration of many layers of functional information simultaneously. Although created for applications in biology, N?Browse uses a generic database schema that can be adapted to network representations in any knowledge domain. The N?Browse client?server package is freely available for distribution, providing a convenient way for data producers and providers to distribute and offer interactive visualization of network?based data. Curr. Protoc. Bioinform. 23:9.11.1?9.11.21. © 2008 by John Wiley & Sons, Inc.
Keywords: network; molecular; interaction; graph; browser; Web?based; client?server system; JAVA; functional genomics; GUI; visualization; database; MySQL
Table of Contents
- Introduction
- Navigating the N‐Browse GUI
- Basic Protocol 1: Basics of the N‐Browse GUI
- Basic Protocol 2: Working with Datasets and User‐Defined Uploads
- Basic Protocol 3: Installing and Configuring the N‐Browse Client‐Server Package
- Basic Protocol 4: Installing and Populating the N‐Browse Generic Database
- Commentary
- Acknowledgements
- Key Reference
- Figures
- Tables
Materials
Figures
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Figure 9.11.1 The N‐Browse GUI. View Image -
Figure 9.11.2 The N‐Browse homepage. View Image -
Figure 9.11.3 Network navigation: sequential expansion around selected network nodes. In this example, the user has entered an initial query par‐6 (A ) and subsequently expands the network around par‐5 (B ) and par‐3 (C ). For demonstration video see the N‐Browse online tutorial. View Image -
Figure 9.11.4 Matrix (A ) and Spoke (B ) views for the query par‐6 in C. elegans at http://gnetbrowse.org. View Image -
Figure 9.11.5 The N‐Browse Advanced Web page. View Image
Videos
Literature Cited
| Lall, S., Grun, D., Krek, A., Chen, K., Wang, Y.L., Dewey, C.N., Sood, P., Colombo, T., Bray, N., MacMenamin, P., Kao, H.L., Gunsalus, K.C., Pachter, L., Piano, F., and Rajewsky, N. 2006. A genome‐wide map of conserved microRNA targets in C. elegans. Curr. Biol. 16: 460‐471. | |
| This is the first article in the literature to describe the use of N‐Browse for integrating a new genome‐scale dataset with other available molecular interaction data. N‐Browse was used to integrate microRNA‐target predictions with multiple types of functional links in C. elegans gathered from a variety of sources (these datasets are described on the gnetbrowse.org Web site). | |
| Internet Resources | |
| http://gnetbrowse.org | |
| The main N‐Browse Web site, currently providing access to heterogeneous functional data in E. coli, C. elegans, D. melanogaster, and H. sapiens (see the Web site for details on available datasets). Provides a link to the downloadable N‐Browse client‐server distribution package. | |
| http://sourceforge.net/projects/nbrowse | |
| The N‐Browse client‐server distribution package can be downloaded from here. | |
| http://www.gmod.org/wiki/index.php/nbrowse | |
| Provides a description of the N‐Browse project with news and links to other N‐Browse resources. | |
| http://www.wormbase.org | |
| The first example of an independent N‐Browse client‐server installation. WormBase currently uses N‐Browse as a graphical interface to server molecular interaction data curated there. Links to the N‐Browse GUI at WormBase are available on the Gene Summary pages. Also see UNIT . | |
| http://interactome.dfci.harvard.edu/C_elegans/host.php | |
| An N‐Browse portal is provided by the CCSB Interactome Database to visualize C. elegans protein‐protein interaction data in the context of other functional genomic data. |
