Linking Cytoscape and the corynebacterial reference database CoryneRegNet.

BMC Genomics
Jan Baumbach, Leonard Apeltsin

Abstract

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 K12 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. We introduce two novel plugins for the Cytoscape environment de...Continue Reading

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Citations

Sep 25, 2012·BMC Bioinformatics·Suzanne M PaleyPeter D Karp
May 28, 2009·BMC Genomics·Carito GuziolowskiAnne Siegel
Jan 9, 2010·BMC Genomics·Jasmin SchröderAndreas Tauch
Jul 28, 2012·International Journal of Molecular Sciences·Vanessa Medina VillaamilLuis M Antón Aparicio
May 24, 2014·Briefings in Functional Genomics·Eudes BarbosaJan Baumbach
Feb 10, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Josch PaulingJan Baumbach
Feb 23, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Nicolas AlcarazJan Baumbach
Aug 25, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Carito GuziolowskiAnne Siegel
Sep 29, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Dong-Guk ShinDavid Rowe
May 7, 2016·Nucleic Acids Research·Markus ListJan Baumbach
Nov 15, 2017·Nucleic Acids Research·Denitsa EckweilerDieter Jahn
Nov 22, 2018·Nucleic Acids Research·Simon J LarsenJan Baumbach

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Software Mentioned

COMA
CoryneRegNet
Cytoscape
RegulonDB
CytoscapePlugin
CoryneRegNetLoader

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