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Updated: Jun 15, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
Characterizing regulatory path motifs in integrated networks using perturbational data
Anagha Joshi1, Thomas Van Parys, Yves Van de Peer
1Department of Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium. anagha.joshi@psb.vib-ugent.be
Abstract:
We introduce Pathicular http://bioinformatics.psb.ugent.be/software/details/Pathicular, a Cytoscape plugin for studying the cellular response to perturbations of transcription factors by integrating perturbational expression data with transcriptional, protein-protein and phosphorylation networks. Pathicular searches for 'regulatory path motifs', short paths in the integrated physical networks which occur significantly more often than expected between transcription factors and their targets in the perturbational data. A case study in Saccharomyces cerevisiae identifies eight regulatory path motifs and demonstrates their biological significance.
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