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GraphWeb is a public web server for graph-based analysis of biological networks that:
  • analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes;
  • integrates multiple diverse datasets into global networks;
  • incorporates multispecies data using gene orthology mapping;
  • filters nodes and edges based on dataset support, edge weight and node annotation;
  • detects gene modules from networks using a collection of algorithms;
  • interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs.
J. Reimand*, L. Tooming*, H. Peterson, P. Adler, J. Vilo: GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. (2008)
Nucl. Acids Res. 2008 36: W452-W459; doi:10.1093/nar/gkn230 [ PDF ]

Recent updates

17 December 2008

The "Sort modules by functional score" option was broken. It is fixed now.

5 October 2008

I discovered today that the Advanced input tool, as well as the Manage data uploads tool, were not working. This has been fixed.

The "View dataset" and "Delete dataset" buttons under Manage data uploads that appear when you log in don't work either. This problem will be fixed in the future.

The extension of the Cytoscape SIF input produced has been changed from .txt to .sif, which should make exporting modules to Cytoscape more comfortable.

14 August 2008

The former Tutorial page has been renamed into Overview, since there is something more like a tutorial on the Help page instead. The language of the overview page has been made clearer at some places.

8 August 2008

In the 5 August version, the g:Cocoa links had stopped working. This error is now fixed.

5 August 2008

By clicking on "get coordinates" in the visualisation screen, you can see the coordinates of the nodes and edges on the current image, as output by Graphviz.

A new feature is available on the summary row in the end of the results table. By clicking on the link "All displayed modules" you can download a list of all modules in one file.

A bug was found and fixed that caused the "All nodes" list in the summary row to be incorrect (the names of some nodes were merged together on one line).

The "Manage data uploads" section (g:PEDaM) can now only be used from the front page, not the results page. This applies to creating a new folder, logging in, uploading new files and deleting existing files in your folder. If you are logged in, your status is remembered and you can access all the features by returning to the front page. Also, your files remain accessible in the menu "From a file in our server" and in the advanced input window. The reason for the change is that trying to use g:PEDaM from the results page caused a refresh of the page, causing the results to be recomputed.

GraphWeb 2007-2008
Laur Tooming & Jüri Reimand & Jaak Vilo @ BIIT Group, Institute of Computer Science, University of Tartu.