Linking Cytoscape and the corynebacterial reference database CoryneRegNet

Baumbach, Jan; Apeltsin, Leonard

doi:10.1186/1471-2164-9-184

Cited by 30 publications

(30 citation statements)

References 16 publications

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“…KeyPathwayMiner was implemented as a Cytoscape 6,9,22 (http://www.cytoscape.org) plugin which is now freely available for download through the Cytoscape's plugin manager or through the project's web site.…”

Section: Analysis Of Colon Cancer Dna Methylation Profilesmentioning

confidence: 99%

Efficient key pathway mining: combining networks and OMICS data

Alcaraz

Friedrich

Kötzing

et al. 2012

Integrative Biology

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Systems biology has emerged over the last decade. Driven by the advances in sophisticated measurement technology the research community generated huge molecular biology data sets. These comprise rather static data on the interplay of biological entities, for instance protein-protein interaction network data, as well as quite dynamic data collected for studying the behavior of individual cells or tissues in accordance with changing environmental conditions, such as DNA microarrays or RNA sequencing. Here we bring the two different data types together in order to gain higher level knowledge. We introduce a significantly improved version of the KeyPathwayMiner software framework. Given a biological network modelled as a graph and a set of expression studies, KeyPathwayMiner efficiently finds and visualizes connected sub-networks where most components are expressed in most cases. It finds all maximal connected sub-networks where all nodes but k exceptions are expressed in all experimental studies but at most l exceptions. We demonstrate the power of the new approach by comparing it to similar approaches with gene expression data previously used to study Huntington's disease. In addition, we demonstrate KeyPathwayMiner's flexibility and applicability to non-array data by analyzing genome-scale DNA methylation profiles from colorectal tumor cancer patients. KeyPathwayMiner release 2 is available as a Cytoscape plugin and online at http://keypathwayminer.mpi-inf.mpg.de.

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Section: Analysis Of Colon Cancer Dna Methylation Profilesmentioning

confidence: 99%

Efficient key pathway mining: combining networks and OMICS data

Alcaraz

Friedrich

Kötzing

et al. 2012

Integrative Biology

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“…In addition, because it is nonpathogenic and grows fast, C. glutamicum is an emerging model system for members of the Corynebacterineae, an Actinomycetes suborder, including Mycobacterium tuberculosis, the causative agent of tuberculosis. In the course of extensive genome-wide analyses, a transcriptional regulatory network model composed of an increasing number of known regulators has been constructed and updated (8,9,56,68). GlxR, which is a CRP-type transcriptional regulator, is one of the most important regulators of C. glutamicum.…”

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confidence: 99%

Genome-Wide Identification of In Vivo Binding Sites of GlxR, a Cyclic AMP Receptor Protein-Type Regulator in Corynebacterium glutamicum

et al. 2011

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Corynebacterium glutamicum GlxR is a cyclic AMP (cAMP) receptor protein-type regulator. Although over 200 GlxR-binding sites in the C. glutamicum genome are predicted in silico, studies on the physiological function of GlxR have been hindered by the severe growth defects of a glxR mutant. This study identified the GlxR regulon by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analyses. In total, 209 regions were detected as in vivo GlxR-binding sites. In vitro binding assays and promoter-reporter assays demonstrated that GlxR directly activates expression of genes for aerobic respiration, ATP synthesis, and glycolysis and that it is required for expression of genes for cell separation and mechanosensitive channels. GlxR also directly represses a citrate uptake gene in the presence of citrate. Moreover, ChIP-chip analyses showed that GlxR was still able to interact with its target sites in a mutant with a deletion of cyaB, the sole adenylate cyclase gene in the genome, even though binding affinity was markedly decreased. Thus, GlxR is physiologically functional at the relatively low cAMP levels in the cyaB mutant, allowing the cyaB mutant to grow much better than the glxR mutant.

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“…In this study, we are convinced that our predictions are more reliable as with C. glutamicum we have an exhaustively studied model organism at hand which is evolutionary very close to Cp [46, 47, 58]. …”

Section: Introductionmentioning

confidence: 65%

“…As prominent example may serve the reconstruction of the regulatory network of various different Corynebacteria which has become a widely used resource [46, 47]. …”

Section: Introductionmentioning

confidence: 99%

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks

et al. 2016

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Background Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis, a chronic infection affecting sheep and goats, causing economic losses due to carcass condemnation and decreased production of meat, wool, and milk. Current diagnosis or treatment protocols are not fully effective and, thus, require further research of Cp pathogenesis.ResultsHere, we mapped known protein-protein interactions (PPI) from various species to nine Cp strains to reconstruct parts of the potential Cp interactome and to identify potentially essential proteins serving as putative drug targets. On average, we predict 16,669 interactions for each of the nine strains (with 15,495 interactions shared among all strains). An in silico sanity check suggests that the potential networks were not formed by spurious interactions but have a strong biological bias. With the inferred Cp networks we identify 181 essential proteins, among which 41 are non-host homologous.ConclusionsThe list of candidate interactions of the Cp strains lay the basis for developing novel hypotheses and designing according wet-lab studies. The non-host homologous essential proteins are attractive targets for therapeutic and diagnostic proposes. They allow for searching of small molecule inhibitors of binding interactions enabling modern drug discovery. Overall, the predicted Cp PPI networks form a valuable and versatile tool for researchers interested in Corynebacterium pseudotuberculosis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0346-4) contains supplementary material, which is available to authorized users.

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Linking Cytoscape and the corynebacterial reference database CoryneRegNet

Cited by 30 publications

References 16 publications

Efficient key pathway mining: combining networks and OMICS data

Efficient key pathway mining: combining networks and OMICS data

Genome-Wide Identification of In Vivo Binding Sites of GlxR, a Cyclic AMP Receptor Protein-Type Regulator in Corynebacterium glutamicum

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks

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