Dataset Information

The Cytoscape BioGateway App: explorative network building from the BioGateway triple store.

ABSTRACT: Summary: The BioGateway App is a Cytoscape (version 3) plugin designed to provide easy query access to the BioGateway RDF triple store, which contains functional and interaction information for proteins from several curated resources. For explorative network building, we have added a comprehensive dataset with regulatory relationships of mammalian DNA binding transcription factors and their target genes, compiled both from curated resources and from a text mining effort. Query results are visualised using the inherent flexibility of the Cytoscape framework, and network links can be checked against curated database records or against the original publication.

Availability: Install through the Cytoscape application manager or visit www.biogateway.eu for download and tutorial documents.

Supplementary information: Supplementary information is available at Bioinformatics online.

SUBMITTER: Holmas S

PROVIDER: S-EPMC7703768 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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The Cytoscape BioGateway App: explorative network building from the BioGateway triple store.

Holmås Stian S Puig Rafel Riudavets RR Acencio Marcio Luis ML Mironov Vladimir V Kuiper Martin M

Bioinformatics (Oxford, England) 20191109

<h4>Summary</h4>The BioGateway App is a Cytoscape (version 3) plugin designed to provide easy query access to the BioGateway RDF triple store, which contains functional and interaction information for proteins from several curated resources. For explorative network building, we have added a comprehensive dataset with regulatory relationships of mammalian DNA binding transcription factors and their target genes, compiled both from curated resources and from a text mining effort. Query results are ...[more]

PMID: 31710663

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Project description:IntroductionThe high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory processes can be obtained. Various databases contain information on the interactions of regulators with their targets for different organisms, data recently being extended with the results of the ENCODE (Encyclopedia of DNA Elements) project. A systems biology approach integrating our understanding on different regulators is essential in interpreting the regulation of molecular biological processes.ImplementationWe developed CyTargetLinker (http://projects.bigcat.unimaas.nl/cytargetlinker), a Cytoscape app, for integrating regulatory interactions in network analysis. Recently we released CyTargetLinker as one of the first apps for Cytoscape 3. It provides a user-friendly and flexible interface to extend biological networks with regulatory interactions, such as microRNA-target, transcription factor-target and/or drug-target. Importantly, CyTargetLinker employs identifier mapping to combine various interaction data resources that use different types of identifiers.ResultsThree case studies demonstrate the strength and broad applicability of CyTargetLinker, (i) extending a mouse molecular interaction network, containing genes linked to diabetes mellitus, with validated and predicted microRNAs, (ii) enriching a molecular interaction network, containing DNA repair genes, with ENCODE transcription factor and (iii) building a regulatory meta-network in which a biological process is extended with information on transcription factor, microRNA and drug regulation.ConclusionsCyTargetLinker provides a simple and extensible framework for biologists and bioinformaticians to integrate different regulatory interactions into their network analysis approaches. Visualization options enable biological interpretation of complex regulatory networks in a graphical way. Importantly the incorporation of our tool into the Cytoscape framework allows the application of CyTargetLinker in combination with a wide variety of other apps for state-of-the-art network analysis.

Project description:BACKGROUND:In the app stores of mobile platforms, consumers are confronted with an enormous number of mobile apps. Over the past few years, considerable research has been undertaken into to identifying, characterizing, and evaluating apps, be it in health-related or other contexts. However, many of these projects are restricted to specific areas of application and offer little flexibility in adapting the applied criteria. OBJECTIVE:This paper presents an adaptable method for selecting and characterizing mobile apps listed in a mobile App Store (the Apple App Store). The method is based on filtering processes using predefined criteria, through a semiautomated retrospective App Store analysis (SARASA). METHODS:To illustrate the SARASA process, keyword-based filtering and metadata-based description, review, and ranking steps were applied to a dataset, more specifically, an April 2018 readout of the Medical category of the German App Store, with the aim of obtaining a list of cardiology-related apps. RESULTS:From the original list of 39,427 apps within the "Medical" category of the App Store on April 14, 2018, 34,382 apps with store descriptions in languages other than German were removed. For the remaining 5045 apps, keywords related to cardiology were applied to filter the output, obtaining a final total of 335 subject-specific apps for further analysis and description. CONCLUSIONS:SARASA provides an easy to use method for applying filtering processes to identify apps matching predefined, formal criteria from app stores. The criteria can be well adapted to the needs of users. Automatic and manual analyses are easily combined when using SARASA. In the future, additional features, such as algorithmic topic analyses, may supplement the process. Although the area of application is currently limited to Apple's App Store, expansion to other stores is planned. The method stands or falls with the transparency of the app store providers and the manufacturers to make relevant meta-information available. It is up to them to liberalize information and restrict censorship to provide clients, customers, and users truly fair circumstances finding their way around the app market.

Dataset Information

The Cytoscape BioGateway App: explorative network building from the BioGateway triple store.

Publications

The Cytoscape BioGateway App: explorative network building from the BioGateway triple store.

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