Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet
Baumbach J, Wittkop T, Kleindt CK, Tauch A (2009)
Nature Protocols 4(6): 992-1005.
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Autor*in
Baumbach, Jan;
Wittkop, Tobias;
Kleindt, Christiane KatjaUniBi;
Tauch, AndreasUniBi
Einrichtung
Abstract / Bemerkung
CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. It provides web-based access to integrated data on gene regulatory interactions of corynebacteria relevant to human medicine and biotechnology, Escherichia coli and Mycobacterium tuberculosis. To facilitate the analysis and reconstruction of the corresponding networks, CoryneRegNet provides user-friendly interfaces for bioinformatics analysis and network visualization tools. This protocol describes four major workflows: (1) querying the regulatory network of a gene of interest, (2) prediction and interspecies transfer of gene regulatory interactions, (3) visualization and comparison of predicted or known networks and (4) integration of gene expression data analysis and visualization. This protocol guides the user through the most important features of CoryneRegNet and takes 45–60 min to complete.
Erscheinungsjahr
2009
Zeitschriftentitel
Nature Protocols
Band
4
Ausgabe
6
Seite(n)
992-1005
ISSN
1754-2189
eISSN
1750-2799
Page URI
https://pub.uni-bielefeld.de/record/1929146
Zitieren
Baumbach J, Wittkop T, Kleindt CK, Tauch A. Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols. 2009;4(6):992-1005.
Baumbach, J., Wittkop, T., Kleindt, C. K., & Tauch, A. (2009). Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols, 4(6), 992-1005. https://doi.org/10.1038/nprot.2009.81
Baumbach, Jan, Wittkop, Tobias, Kleindt, Christiane Katja, and Tauch, Andreas. 2009. “Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet”. Nature Protocols 4 (6): 992-1005.
Baumbach, J., Wittkop, T., Kleindt, C. K., and Tauch, A. (2009). Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols 4, 992-1005.
Baumbach, J., et al., 2009. Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols, 4(6), p 992-1005.
J. Baumbach, et al., “Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet”, Nature Protocols, vol. 4, 2009, pp. 992-1005.
Baumbach, J., Wittkop, T., Kleindt, C.K., Tauch, A.: Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols. 4, 992-1005 (2009).
Baumbach, Jan, Wittkop, Tobias, Kleindt, Christiane Katja, and Tauch, Andreas. “Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet”. Nature Protocols 4.6 (2009): 992-1005.
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Addressing the problems with life-science databases for traditional uses and systems biology.
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Fast index based algorithms and software for matching position specific scoring matrices.
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Protein families and TRIBES in genome sequence space.
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Spectral clustering of protein sequences.
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Clustering by passing messages between data points.
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EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
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The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum.
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AUTHOR UNKNOWN, 0
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms.
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Integration of biological networks and gene expression data using Cytoscape.
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Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
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The glycosylated cell surface protein Rpf2, containing a resuscitation-promoting factor motif, is involved in intercellular communication of Corynebacterium glutamicum.
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GenDB--an open source genome annotation system for prokaryote genomes.
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