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Characterizing regulatory path motifs in integrated networks using perturbational data.

Joshi A, Van Parys T, Peer YV, Michoel T - Genome Biol. (2010)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department 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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A screenshot of Pathicular. Screenshot of Pathicular running in Cytoscape with an example of a TRI-TRI path motif overrepresented in deletion data for the transcription factor SWI4. Solid edges represent TRI edges, colored by path module membership. Dashed edges represent edges in the deletion data. Solid gray edges are additional TRI edges which do not belong to a TRI-TRI motif in this subnetwork.
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Figure 5: A screenshot of Pathicular. Screenshot of Pathicular running in Cytoscape with an example of a TRI-TRI path motif overrepresented in deletion data for the transcription factor SWI4. Solid edges represent TRI edges, colored by path module membership. Dashed edges represent edges in the deletion data. Solid gray edges are additional TRI edges which do not belong to a TRI-TRI motif in this subnetwork.

Mentions: Figure 5 shows a screenshot of Pathicular with a TRI-TRI path motif overrepresented in deletion data for the transcription factor SWI4. Sample data and step-by-step instructions for running Pathicular are provided in Additional File 2.


Characterizing regulatory path motifs in integrated networks using perturbational data.

Joshi A, Van Parys T, Peer YV, Michoel T - Genome Biol. (2010)

A screenshot of Pathicular. Screenshot of Pathicular running in Cytoscape with an example of a TRI-TRI path motif overrepresented in deletion data for the transcription factor SWI4. Solid edges represent TRI edges, colored by path module membership. Dashed edges represent edges in the deletion data. Solid gray edges are additional TRI edges which do not belong to a TRI-TRI motif in this subnetwork.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864572&req=5

Figure 5: A screenshot of Pathicular. Screenshot of Pathicular running in Cytoscape with an example of a TRI-TRI path motif overrepresented in deletion data for the transcription factor SWI4. Solid edges represent TRI edges, colored by path module membership. Dashed edges represent edges in the deletion data. Solid gray edges are additional TRI edges which do not belong to a TRI-TRI motif in this subnetwork.
Mentions: Figure 5 shows a screenshot of Pathicular with a TRI-TRI path motif overrepresented in deletion data for the transcription factor SWI4. Sample data and step-by-step instructions for running Pathicular are provided in Additional File 2.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department 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.

Show MeSH