Characterizing regulatory path motifs in integrated networks using perturbational data.
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.
Joshi
Anagha
A
Department of Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium. anagha.joshi@psb.vib-ugent.be
Van Parys
Thomas
T
Van de Peer
Yves
Y
Michoel
Tom
T
D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae; D015398:Signal Transduction / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
D014157:Transcription Factors