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Updated: Jun 9, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
Published on: March 7, 2018
Global modeling of transcriptional responses in interaction networks
Leo Lahti1, Juha E A Knuuttila, Samuel Kaski
1Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science and Technology, Aalto, Finland. leo.lahti@iki.fi
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 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 at http://www.cis.hut.fi/projects/mi/software/NetResponse
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