  Integrating expression data with gene interactions in a network is essential
for understanding the functional organization of the cells. Consequently,
knowledge of interaction types in biological networks is important for data
interpretation. Signing of Regulatory Networks (SIREN) plugin for Cytoscape is
an open-source Java tool for discrimination of interaction type (activatory or
inhibitory) in gene regulatory networks. Utilizing an information theory based
concept, SIREN seeks to identify the interaction type of pairs of genes by
examining their corresponding gene expression profiles. We introduce SIREN, a
fast and memory efficient tool with low computational complexity, that allows
the user to easily consider it as a complementary approach for many network
reconstruction methods. SIREN allows biologists to use independent expression
data to predict interaction types for known gene regulatory networks where
reconstruction methods do not provide any information about the nature of their
interaction types. The SIREN Cytoscape plugin is implemented in Java and is
freely available at http://baderlab.org/Software/SIRENplugin and via the
Cytoscape app manager.
