Announcing: ExprEssence Cytoscape plugin for differential data visualization
Gregor Warsow
Cytoscape.
ExprEssence helps to identify those links (edges) in a network which
are influenced most strongly in the transition from one experimental
condition to another. The user simply has to integrate his/her data
(e.g. gene expression or protein abundance data) representing two
conditions of interest into the network. ExprEssence then calculates a
score for each link which describes the amount of change along the
link. The link score method is described here:
http://www.biomedcentral.com/1752-0509/4/164
ExprEssence reduces the network (by removal of edges and nodes) down
to a level defined by the user, which can easily be done by setting
link score thresholds with a slider. Then, the user can interactively
investigate the most prominent changes occurring in the transition
from the first to the second condition.
Hence, ExprEssence allows to identify most promising links which may
describe mechanisms that could explain the difference between the two
conditions.
During the last 12 months since publication, our plugin has been used
for a large set of applications such as:
* Comparing responders and non-responders to breast cancer
chemotherapy
* Investigating the effect of DHEA in Sjögren's Syndrome
* Tracking the mechanisms behind neuronal differentiation
* Comparing fibrotic and non-fibrotic tissue
We are thus confident that it may be useful for a wide variety of
differential analyses.
ExprEssence is available via the plugin manager under the Analysis
category, or directly from SourceForge:
http://sourceforge.net/projects/expressence/