ArticleBMC genomics2008
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
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- Genome-wide identification of in vivo binding sites of GlxR, a cyclic AMP receptor protein-type regulator in Corynebacterium glutamicum.Journal of bacteriology · 2011Article
- On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks.Nucleic acids research · 2010Review
- Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.BMC systems biology · 2010Article
- The Zur regulon of Corynebacterium glutamicum ATCC 13032.BMC genomics · 2010Article
- BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks.BMC genomics · 2009Article
- Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet.Nature protocols · 2009Article
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Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundRecently, 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.
resultsWe 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. CoryneRegNetLoader 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.
conclusionThe 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 most-widely used tools for biological network analyses.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.