Global modeling of transcriptional responses in interaction networks. Bioinformatics 26(21):2713-20 Preprint available at: http://www.cis.hut.fi/lmlahti/publications/Lahti10bioinf-preprint.pdf

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 tran-scriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms between tissues, and potentially as yet unknown processes. The same method can also be applied to cell-biological conditions in one or more tissues. Results: 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 tissues. 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 tissues, and coordinated, context-specific regulation of the genes. Availability: Implementation is freely available in R and Matlab a