Global modeling of transcriptional responses in interaction networks.
BACKGROUND
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 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.


BACKGROUND
Implementation is freely available in R and Matlab at http://www.cis.hut.fi/projects/mi/software/NetResponse
Lahti
Leo
L
Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, Aalto, Finland. leo.lahti@iki.fi
Knuuttila
Juha E A
JE
Kaski
Samuel
S
D030541:Databases, Genetic; D053263:Gene Regulatory Networks / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D014158:Transcription, Genetic / Q000235:genetics*