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Inferring the transcriptional network of Bacillus subtilis

Abeer Fadda, Ana Carolina Fierro, Karen Lemmens, Pieter Monsieurs, Kristof Engelen and Kathleen Marchal (UGent)
(2009) MOLECULAR BIOSYSTEMS. 5(12). p.1840-1852
Author
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Abstract
The adaptation of bacteria to the vigorous environmental changes they undergo is crucial to their survival. They achieve this adaptation partly via intricate regulation of the transcription of their genes. In this study, we infer the transcriptional network of the Gram-positive model organism, Bacillus subtilis. We use a data integration workflow, exploiting both motif and expression data, towards the generation of condition-dependent transcriptional modules. In building the motif data, we rely on both known and predicted information. Known motifs were derived from DBTBS, while predicted motifs were generated by a de novo motif detection method that utilizes comparative genomics. The expression data consists of a compendium of microarrays across different platforms. Our results indicate that a considerable part of the B. subtilis network is yet undiscovered; we could predict 417 new regulatory interactions for known regulators and 453 interactions for yet uncharacterized regulators. The regulators in our network showed a preference for regulating modules in certain environmental conditions. Also, substantial condition-dependent intra-operonic regulation seems to take place. Global regulators seem to require functional flexibility to attain their roles by acting as both activators and repressors.
Keywords
ESCHERICHIA-COLI, AMINO-ACID-TRANSPORT, REGULATORY NETWORK, GENE-EXPRESSION, HIERARCHICAL STRUCTURE, COEXPRESSED GENES, GENOMIC ANALYSIS, MOTIFS, SPORULATION, DATABASE

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MLA
Fadda, Abeer, et al. “Inferring the Transcriptional Network of Bacillus Subtilis.” MOLECULAR BIOSYSTEMS, vol. 5, no. 12, 2009, pp. 1840–52, doi:10.1039/b907310h.
APA
Fadda, A., Fierro, A. C., Lemmens, K., Monsieurs, P., Engelen, K., & Marchal, K. (2009). Inferring the transcriptional network of Bacillus subtilis. MOLECULAR BIOSYSTEMS, 5(12), 1840–1852. https://doi.org/10.1039/b907310h
Chicago author-date
Fadda, Abeer, Ana Carolina Fierro, Karen Lemmens, Pieter Monsieurs, Kristof Engelen, and Kathleen Marchal. 2009. “Inferring the Transcriptional Network of Bacillus Subtilis.” MOLECULAR BIOSYSTEMS 5 (12): 1840–52. https://doi.org/10.1039/b907310h.
Chicago author-date (all authors)
Fadda, Abeer, Ana Carolina Fierro, Karen Lemmens, Pieter Monsieurs, Kristof Engelen, and Kathleen Marchal. 2009. “Inferring the Transcriptional Network of Bacillus Subtilis.” MOLECULAR BIOSYSTEMS 5 (12): 1840–1852. doi:10.1039/b907310h.
Vancouver
1.
Fadda A, Fierro AC, Lemmens K, Monsieurs P, Engelen K, Marchal K. Inferring the transcriptional network of Bacillus subtilis. MOLECULAR BIOSYSTEMS. 2009;5(12):1840–52.
IEEE
[1]
A. Fadda, A. C. Fierro, K. Lemmens, P. Monsieurs, K. Engelen, and K. Marchal, “Inferring the transcriptional network of Bacillus subtilis,” MOLECULAR BIOSYSTEMS, vol. 5, no. 12, pp. 1840–1852, 2009.
@article{3186890,
  abstract     = {{The adaptation of bacteria to the vigorous environmental changes they undergo is crucial to their survival. They achieve this adaptation partly via intricate regulation of the transcription of their genes. In this study, we infer the transcriptional network of the Gram-positive model organism, Bacillus subtilis. We use a data integration workflow, exploiting both motif and expression data, towards the generation of condition-dependent transcriptional modules. In building the motif data, we rely on both known and predicted information. Known motifs were derived from DBTBS, while predicted motifs were generated by a de novo motif detection method that utilizes comparative genomics. The expression data consists of a compendium of microarrays across different platforms. Our results indicate that a considerable part of the B. subtilis network is yet undiscovered; we could predict 417 new regulatory interactions for known regulators and 453 interactions for yet uncharacterized regulators. The regulators in our network showed a preference for regulating modules in certain environmental conditions. Also, substantial condition-dependent intra-operonic regulation seems to take place. Global regulators seem to require functional flexibility to attain their roles by acting as both activators and repressors.}},
  author       = {{Fadda, Abeer and Fierro, Ana Carolina and Lemmens, Karen and Monsieurs, Pieter and Engelen, Kristof and Marchal, Kathleen}},
  issn         = {{1742-206X}},
  journal      = {{MOLECULAR BIOSYSTEMS}},
  keywords     = {{ESCHERICHIA-COLI,AMINO-ACID-TRANSPORT,REGULATORY NETWORK,GENE-EXPRESSION,HIERARCHICAL STRUCTURE,COEXPRESSED GENES,GENOMIC ANALYSIS,MOTIFS,SPORULATION,DATABASE}},
  language     = {{eng}},
  number       = {{12}},
  pages        = {{1840--1852}},
  title        = {{Inferring the transcriptional network of Bacillus subtilis}},
  url          = {{http://doi.org/10.1039/b907310h}},
  volume       = {{5}},
  year         = {{2009}},
}
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