Software
Characterizing regulatory path motifs in integrated networks using perturbational data
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* Corresponding author: Tom Michoel tom.michoel@psb.vib-ugent.be
1 Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
2 Department of Plant Biotechnology and Genetics, UGent, Technologiepark 927, B-9052 Gent, Belgium
Genome Biology 2010, 11:R32 doi:10.1186/gb-2010-11-3-r32
Published: 11 March 2010Abstract
We introduce Pathicular http://bioinformatics.psb.ugent.be/software/details/Pathicular webcite, 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.