The condition-dependent transcriptional network in Escherichia coli
- Author
- Karen Lemmens, Tijl De Bie (UGent) , Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen and Kathleen Marchal (UGent)
- Organization
- Abstract
- Thanks to the availability of high-throughput omics data, bioinformatics approaches are able to hypothesize thus-far undocumented genetic interactions. However, due to the amount of noise in these data, inferences based on a single data source are often unreliable. A popular approach to overcome this problem is to integrate different data sources. In this study, we describe DISTILLER, a novel frame work for data integration that simultaneously analyzes microarray and motif information to find modules that: consist. of genes that are co-expressed in a subset of conditions, and their corresponding regulators. By applying our method on publicly available data, we evaluated the condition-specific transcriptional network of Escherichia coli. DISTILLER confirmed 62% of 736 interactions described in RegulonDB, and 278 novel interactions v,,ere predicted.
- Keywords
- REGULATORY NETWORK, EXPRESSION PROFILES, frequent itemset mining, DISTILLER, transcriptional modules, DATABASE, TOOLS
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-3186950
- MLA
- Lemmens, Karen, et al. “The Condition-Dependent Transcriptional Network in Escherichia Coli.” Annals of the New York Academy of Sciences, edited by G Stolovitzky et al., vol. 1158, Wiley-Blackwell, 2009, pp. 29–35, doi:10.1111/j.1749-6632.2008.03746.x.
- APA
- Lemmens, K., De Bie, T., Dhollander, T., Monsieurs, P., De Moor, B., Collado-Vides, J., … Marchal, K. (2009). The condition-dependent transcriptional network in Escherichia coli. Annals of the New York Academy of Sciences, 1158, 29–35. https://doi.org/10.1111/j.1749-6632.2008.03746.x
- Chicago author-date
- Lemmens, Karen, Tijl De Bie, Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen, and Kathleen Marchal. 2009. “The Condition-Dependent Transcriptional Network in Escherichia Coli.” Edited by G Stolovitzky, P Kahlem, and A Califano. Annals of the New York Academy of Sciences 1158: 29–35. https://doi.org/10.1111/j.1749-6632.2008.03746.x.
- Chicago author-date (all authors)
- Lemmens, Karen, Tijl De Bie, Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen, and Kathleen Marchal. 2009. “The Condition-Dependent Transcriptional Network in Escherichia Coli.” Ed by. G Stolovitzky, P Kahlem, and A Califano. Annals of the New York Academy of Sciences 1158: 29–35. doi:10.1111/j.1749-6632.2008.03746.x.
- Vancouver
- 1.Lemmens K, De Bie T, Dhollander T, Monsieurs P, De Moor B, Collado-Vides J, et al. The condition-dependent transcriptional network in Escherichia coli. Stolovitzky G, Kahlem P, Califano A, editors. Annals of the New York Academy of Sciences. 2009;1158:29–35.
- IEEE
- [1]K. Lemmens et al., “The condition-dependent transcriptional network in Escherichia coli,” Annals of the New York Academy of Sciences, vol. 1158, pp. 29–35, 2009.
@article{3186950,
abstract = {{Thanks to the availability of high-throughput omics data, bioinformatics approaches are able to hypothesize thus-far undocumented genetic interactions. However, due to the amount of noise in these data, inferences based on a single data source are often unreliable. A popular approach to overcome this problem is to integrate different data sources. In this study, we describe DISTILLER, a novel frame work for data integration that simultaneously analyzes microarray and motif information to find modules that: consist. of genes that are co-expressed in a subset of conditions, and their corresponding regulators. By applying our method on publicly available data, we evaluated the condition-specific transcriptional network of Escherichia coli. DISTILLER confirmed 62% of 736 interactions described in RegulonDB, and 278 novel interactions v,,ere predicted.}},
author = {{Lemmens, Karen and De Bie, Tijl and Dhollander, Thomas and Monsieurs, Pieter and De Moor, Bart and Collado-Vides, Julio and Engelen, Kristof and Marchal, Kathleen}},
editor = {{Stolovitzky, G and Kahlem, P and Califano, A}},
isbn = {{9781573317511}},
issn = {{0077-8923}},
journal = {{Annals of the New York Academy of Sciences}},
keywords = {{REGULATORY NETWORK,EXPRESSION PROFILES,frequent itemset mining,DISTILLER,transcriptional modules,DATABASE,TOOLS}},
language = {{eng}},
location = {{Madrid, Spain}},
pages = {{29--35}},
publisher = {{Wiley-Blackwell}},
title = {{The condition-dependent transcriptional network in Escherichia coli}},
url = {{http://dx.doi.org/10.1111/j.1749-6632.2008.03746.x}},
volume = {{1158}},
year = {{2009}},
}
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