  Motivation: Cell-biological processes are regulated through a complex network
of interactions between genes and their products. The processes, their
activating conditions, and the associated transcriptional responses are often
unknown. Organism-wide modeling of network activation can reveal unique and
shared mechanisms between physiological conditions, and potentially as yet
unknown processes. We introduce a novel approach for organism-wide discovery
and analysis of transcriptional responses in interaction networks. The method
searches for local, connected regions in a network that exhibit coordinated
transcriptional response in a subset of conditions. Known interactions between
genes are used to limit the search space and to guide the analysis. Validation
on a human pathway network reveals physiologically coherent responses,
functional relatedness between physiological conditions, and coordinated,
context-specific regulation of the genes. Availability: Implementation is
freely available in R and Matlab at http://netpro.r-forge.r-project.org
