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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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Relative abundance of path motifs in conditional networks. The relative fraction of each regulatory path motif in deletion data under DNA-damage stress (left) and cell cycle (right). These show differences in network structure under different conditions.
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Figure 7: Relative abundance of path motifs in conditional networks. The relative fraction of each regulatory path motif in deletion data under DNA-damage stress (left) and cell cycle (right). These show differences in network structure under different conditions.

Mentions: In [1], it was shown that large changes occur in the network architecture underlying exogenous and endogenous processes. More precisely, it was observed that environmental responses prefer fast signal propagation with short regulatory cascades, while cell cycle and sporulation direct temporal progression through multiple stages with highly interconnected transcription factors [1]. To see the effect of these differences on the relative abundance of each path motif, we considered two condition dependent deletion networks, one cell cycle specific and the other under DNA-damage condition (see Methods for details). In agreement with [1], in the DNA-damage network, more that 75% of the paths are of path length one or two, while the cell cycle network contains a large fraction of indirect paths with more than 50% formed by paths of length three (Figure 7).


Characterizing regulatory path motifs in integrated networks using perturbational data.

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

Relative abundance of path motifs in conditional networks. The relative fraction of each regulatory path motif in deletion data under DNA-damage stress (left) and cell cycle (right). These show differences in network structure under different conditions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Relative abundance of path motifs in conditional networks. The relative fraction of each regulatory path motif in deletion data under DNA-damage stress (left) and cell cycle (right). These show differences in network structure under different conditions.
Mentions: In [1], it was shown that large changes occur in the network architecture underlying exogenous and endogenous processes. More precisely, it was observed that environmental responses prefer fast signal propagation with short regulatory cascades, while cell cycle and sporulation direct temporal progression through multiple stages with highly interconnected transcription factors [1]. To see the effect of these differences on the relative abundance of each path motif, we considered two condition dependent deletion networks, one cell cycle specific and the other under DNA-damage condition (see Methods for details). In agreement with [1], in the DNA-damage network, more that 75% of the paths are of path length one or two, while the cell cycle network contains a large fraction of indirect paths with more than 50% formed by paths of length three (Figure 7).

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