Linking Cytoscape and the corynebacterial reference database CoryneRegNet

Baumbach J, Apeltsin L (2008)
BMC Genomics 9(1).

Download
OA
Journal Article | Published | English
Author
;
Abstract
Background: Recently, the research community has seen an influx of data relating to transcriptional regulatory interactions of Corynebacteria, organisms that are highly relevant to fields of systems biology, biotechnology, and human medicine. Information derived from DNA microarray experiments, computational predictions, and literature has opened the way for the graph-based analysis, visualization, and reconstruction of transcriptional regulatory networks across entire organisms. The reference database for corynebacterial gene regulatory networks CoryneRegNet provides methods for data storage and data exchange in a well-structured manner. Additional information on the model organism Escherichia coli KI2 obtained from RegulonDB has been integrated. Generally, gene regulatory networks can be visualized as graphs by drawing directed edges between nodes, where a node represents a gene and an edge corresponds to a typed regulatory interaction. Cytoscape is an open-source software project whose aim is to provide graph-based visualization and analysis for biological networks. Its architecture allows the development and integration of user-made plugins to enhance core functionalities. Results: We introduce two novel plugins for the Cytoscape environment designed to enhance in silico studies of procaryotic transcriptional regulatory networks. Our plugins leverage the information from the cornyebacterial reference database CoryneRegNet with the graph analysis capabilities of Cytoscape. CoryneRegNet Loader queries the CoryneRegNet database to extract a gene regulatory network represented as a directed graph. Additional information is stored as node/edge attributes within the graph. COMA facilitates consistency checks for gene expression studies given a gene regulatory network. COMA tests whether all gene expression levels correlate properly with the given network topology. Conclusion: The plugins facilitate in silico studies of procaryotic transcriptional gene regulation, particularly in Corynebacteria and E. coli, by combining the knowledge from the corynebacterial reference database with the graph analysis capabilities of Cytoscape, which is one of the mostwidely used tools for biological network analyses.
Publishing Year
ISSN
PUB-ID

Cite this

Baumbach J, Apeltsin L. Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008;9(1).
Baumbach, J., & Apeltsin, L. (2008). Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics, 9(1).
Baumbach, J., and Apeltsin, L. (2008). Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics 9.
Baumbach, J., & Apeltsin, L., 2008. Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics, 9(1).
J. Baumbach and L. Apeltsin, “Linking Cytoscape and the corynebacterial reference database CoryneRegNet”, BMC Genomics, vol. 9, 2008.
Baumbach, J., Apeltsin, L.: Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 9, (2008).
Baumbach, Jan, and Apeltsin, Leonard. “Linking Cytoscape and the corynebacterial reference database CoryneRegNet”. BMC Genomics 9.1 (2008).
Main File(s)
File Name
Access Level
OA Open Access

This data publication is cited in the following publications:
This publication cites the following data publications:

14 Citations in Europe PMC

Data provided by Europe PubMed Central.

CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks.
Kittas A, Barozet A, Sereshti J, Grabe N, Tsoka S., BMC Syst Biol 9(), 2015
PMID: 26163265
On the limits of computational functional genomics for bacterial lifestyle prediction.
Barbosa E, Rottger R, Hauschild AC, Azevedo V, Baumbach J., Brief Funct Genomics 13(5), 2014
PMID: 24855068
Regulatory network operations in the Pathway Tools software.
Paley SM, Latendresse M, Karp PD., BMC Bioinformatics 13(), 2012
PMID: 22998532
State of the art in silico tools for the study of signaling pathways in cancer.
Villaamil VM, Gallego GA, Cainzos IS, Valladares-Ayerbes M, Anton Aparicio LM., Int J Mol Sci 13(6), 2012
PMID: 22837650
Designing logical rules to model the response of biomolecular networks with complex interactions: an application to cancer modeling.
Guziolowski C, Blachon S, Baumuratova T, Stoll G, Radulescu O, Siegel A., IEEE/ACM Trans Comput Biol Bioinform 8(5), 2011
PMID: 20733239
Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.
Baumuratova T, Surdez D, Delyon B, Stoll G, Delattre O, Radulescu O, Siegel A., BMC Syst Biol 4(), 2010
PMID: 21044309
The Zur regulon of Corynebacterium glutamicum ATCC 13032.
Schroder J, Jochmann N, Rodionov DA, Tauch A., BMC Genomics 11(), 2010
PMID: 20055984
Computing consistency between microarray data and known gene regulation relationships.
Shin DG, Kazmi SA, Pei B, Kim YA, Maddox J, Nori R, Wong A, Krueger W, Rowe D., IEEE Trans Inf Technol Biomed 13(6), 2009
PMID: 19783507
BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks.
Guziolowski C, Bourde A, Moreews F, Siegel A., BMC Genomics 10(), 2009
PMID: 19470162
Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays.
Jochmann N, Kurze AK, Czaja LF, Brinkrolf K, Brune I, Huser AT, Hansmeier N, Puhler A, Borovok I, Tauch A., Microbiology (Reading, Engl.) 155(Pt 5), 2009
PMID: 19372162
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.
Baumbach J, Tauch A, Rahmann S., Brief. Bioinformatics 10(1), 2009
PMID: 19074493

19 References

Data provided by Europe PubMed Central.

The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.
Perez-Rueda E, Collado-Vides J., Nucleic Acids Res. 28(8), 2000
PMID: 10734204
Reconstruction of microbial transcriptional regulatory networks.
Herrgard MJ, Covert MW, Palsson BO., Curr. Opin. Biotechnol. 15(1), 2004
PMID: 15102470
Emerging Corynebacterium glutamicum systems biology.
Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W., J. Biotechnol. 124(1), 2006
PMID: 16406159
CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.
Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A., BMC Genomics 7(), 2006
PMID: 16478536
CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes
Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S., 2006
CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.
Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A., J. Biotechnol. 129(2), 2007
PMID: 17229482
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J., Nucleic Acids Res. 36(Database issue), 2008
PMID: 18158297
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, Santos-Zavaleta A, Martinez-Flores I, Jimenez-Jacinto V, Bonavides-Martinez C, Segura-Salazar J, Martinez-Antonio A, Collado-Vides J., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381895
Integration of biological networks and gene expression data using Cytoscape.
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD., Nat Protoc 2(10), 2007
PMID: 17947979
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
Cytoscape website
AUTHOR UNKNOWN, 0
Cytoscape plugins website
AUTHOR UNKNOWN, 0
Cytoscape plugin tutorial website
AUTHOR UNKNOWN, 0
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Huser AT, Kalinowski J, Oehm S, Puhler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
PMID: 18034885
Structure and function of the feed-forward loop network motif.
Mangan S, Alon U., Proc. Natl. Acad. Sci. U.S.A. 100(21), 2003
PMID: 14530388
Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.
Gutierrez-Rios RM, Rosenblueth DA, Loza JA, Huerta AM, Glasner JD, Blattner FR, Collado-Vides J., Genome Res. 13(11), 2003
PMID: 14597655

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 18426593
PubMed | Europe PMC

Search this title in

Google Scholar