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  1. Article ; Online: Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs.

    Muetze, Tanja / Lynn, David J

    Current protocols in bioinformatics

    2017  Volume 59, Page(s) 8.24.1–8.24.13

    Abstract: Highly connected nodes in biological networks are called network hubs. Hubs are topologically important to the structure of the network and have been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of ...

    Abstract Highly connected nodes in biological networks are called network hubs. Hubs are topologically important to the structure of the network and have been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we provide a step-by-step protocol for using the Contextual Hub Analysis Tool (CHAT), an application within Cytoscape 3, which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene or protein expression data, and identify hub nodes that are more highly connected to contextual nodes than expected by chance. © 2017 by John Wiley & Sons, Inc.
    MeSH term(s) Computational Biology/methods ; Databases, Genetic ; Gene Regulatory Networks/genetics ; Proteins/genetics ; Software
    Chemical Substances Proteins
    Language English
    Publishing date 2017-09-13
    Publishing country United States
    Document type Journal Article
    ISSN 1934-340X
    ISSN (online) 1934-340X
    DOI 10.1002/cpbi.35
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.

    Ono, Keiichiro / Muetze, Tanja / Kolishovski, Georgi / Shannon, Paul / Demchak, Barry

    F1000Research

    2015  Volume 4, Page(s) 478

    Abstract: As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and ... ...

    Abstract As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST's API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.
    Language English
    Publishing date 2015-08-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.6767.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: CyREST

    Keiichiro Ono / Tanja Muetze / Georgi Kolishovski / Paul Shannon / Barry Demchak

    F1000Research, Vol

    Turbocharging Cytoscape Access for External Tools via a RESTful API [v1; ref status: indexed, http://f1000r.es/5ly]

    2015  Volume 4

    Abstract: As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and ... ...

    Abstract As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.
    Keywords Bioinformatics ; Medicine ; R ; Science ; Q
    Subject code 020
    Language English
    Publishing date 2015-08-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

    Muetze, Tanja / Goenawan, Ivan H / Wiencko, Heather L / Bernal-Llinares, Manuel / Bryan, Kenneth / Lynn, David J

    F1000Research

    2016  Volume 5, Page(s) 1745

    Abstract: Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, ... ...

    Abstract Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such
    Availability: CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store ( http://apps.cytoscape.org/apps/chat).
    Language English
    Publishing date 2016-07-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.9118.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Contextual Hub Analysis Tool (CHAT)

    Tanja Muetze / Ivan H. Goenawan / Heather L. Wiencko / Manuel Bernal-Llinares / Kenneth Bryan / David J. Lynn

    F1000Research, Vol

    A Cytoscape app for identifying contextually relevant hubs in biological networks [version 2; referees: 2 approved]

    2016  Volume 5

    Abstract: Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, ... ...

    Abstract Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest. Availability: CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store (http://apps.cytoscape.org/apps/chat).
    Keywords Bioinformatics ; Tropical & Travel-Associated Diseases ; Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2016-08-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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