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Characterizing regulatory path motifs in integrated networks using perturbational data

Anagha Madhusudan Joshi (UGent) , Thomas Van Parys (UGent) , Yves Van de Peer (UGent) and Tom Michoel (UGent)
(2010) GENOME BIOLOGY. 11(3).
Author
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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.
Keywords
GENOME, YEAST, GENE-EXPRESSION, TRANSCRIPTIONAL REGULATION, ESCHERICHIA-COLI, CELL-CYCLE, SACCHAROMYCES-CEREVISIAE, COMPLEX, DNA, PHOSPHORYLATION

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Citation

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Chicago
Joshi, Anagha Madhusudan, Thomas Van Parys, Yves Van de Peer, and Tom Michoel. 2010. “Characterizing Regulatory Path Motifs in Integrated Networks Using Perturbational Data.” Genome Biology 11 (3).
APA
Joshi, A. M., Van Parys, T., Van de Peer, Y., & Michoel, T. (2010). Characterizing regulatory path motifs in integrated networks using perturbational data. GENOME BIOLOGY, 11(3).
Vancouver
1.
Joshi AM, Van Parys T, Van de Peer Y, Michoel T. Characterizing regulatory path motifs in integrated networks using perturbational data. GENOME BIOLOGY. 2010;11(3).
MLA
Joshi, Anagha Madhusudan, Thomas Van Parys, Yves Van de Peer, et al. “Characterizing Regulatory Path Motifs in Integrated Networks Using Perturbational Data.” GENOME BIOLOGY 11.3 (2010): n. pag. Print.
@article{980143,
  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.},
  articleno    = {R32},
  author       = {Joshi, Anagha Madhusudan and Van Parys, Thomas and Van de Peer, Yves and Michoel, Tom},
  issn         = {1474-760X},
  journal      = {GENOME BIOLOGY},
  language     = {eng},
  number       = {3},
  pages        = {14},
  title        = {Characterizing regulatory path motifs in integrated networks using perturbational data},
  url          = {http://dx.doi.org/10.1186/gb-2010-11-3-r32},
  volume       = {11},
  year         = {2010},
}
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