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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
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ESCHERICHIA-COLI, AMINO-ACID-TRANSPORT, REGULATORY NETWORK, GENE-EXPRESSION, HIERARCHICAL STRUCTURE, COEXPRESSED GENES, GENOMIC ANALYSIS, MOTIFS, SPORULATION, DATABASE
journal title
MOLECULAR BIOSYSTEMS
Mol. Biosyst.
volume
5
issue
12
pages
1840 - 1852
Web of Science type
Article
Web of Science id
000271727600042
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
4.015 (2009)
JCR rank
72/281 (2009)
JCR quartile
1 (2009)
ISSN
1742-206X
DOI
10.1039/b907310h
language
English
UGent publication?
no
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
3186890
handle
http://hdl.handle.net/1854/LU-3186890
date created
2013-04-08 16:30:10
date last changed
2016-12-19 15:39:25
@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},
  keyword      = {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://dx.doi.org/10.1039/b907310h},
  volume       = {5},
  year         = {2009},
}

Chicago
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.
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.
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.
MLA
Fadda, Abeer, Ana Carolina Fierro, Karen Lemmens, et al. “Inferring the Transcriptional Network of Bacillus Subtilis.” MOLECULAR BIOSYSTEMS 5.12 (2009): 1840–1852. Print.