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MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.

Launay G, Salza R, Multedo D, Thierry-Mieg N, Ricard-Blum S - Nucleic Acids Res. (2014)

Bottom Line: Filters may be applied to build sub-networks based on a list of biomolecules, a specified interaction detection method and/or an expression level by tissue, developmental stage, and health state (UniGene data).Any molecule of the network may be selected and its partners added to the network at any time.Networks may be exported under Cytoscape and tabular formats and as images, and may be saved for subsequent re-use.

View Article: PubMed Central - PubMed

Affiliation: UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France.

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Visualization of a network in iNavigator. The navigation bar features a search box. The list of results can be toggled between hits found in MatrixDB or hits found in the displayed network. A button in the top-right corner is used to export the current network or reload a previously saved network. On the left-hand side, buttons provide access to the four main widgets: the tabular network widget, the cart, the network filter widget and a palette widget to change the color of selected nodes. The bottom-right ‘magnifying glass’ widget keeps track of recently visited network elements and allows for the quick inspection of biomolecules and interactions. Hovering the mouse over a node or edge in the network adds that node or edge to the ‘recently visited’ list.
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Figure 3: Visualization of a network in iNavigator. The navigation bar features a search box. The list of results can be toggled between hits found in MatrixDB or hits found in the displayed network. A button in the top-right corner is used to export the current network or reload a previously saved network. On the left-hand side, buttons provide access to the four main widgets: the tabular network widget, the cart, the network filter widget and a palette widget to change the color of selected nodes. The bottom-right ‘magnifying glass’ widget keeps track of recently visited network elements and allows for the quick inspection of biomolecules and interactions. Hovering the mouse over a node or edge in the network adds that node or edge to the ‘recently visited’ list.

Mentions: When browsing MatrixDB, the user can select any publication, biomolecule or UniProtKB keyword and build the corresponding interaction network via iNavigator, a novel interactome network navigator we have developed (Figure 3). The selected items are collected in a cart, which is available on all MatrixDB web pages, and can be deleted from the cart at any time. Interaction networks may be modified either by changing the cart content or by clicking and dragging elements directly on the network. The network can be expanded either by adding the partners and interactions of biomolecules selected within the displayed network, or by querying MatrixDB via the search bar for further publications, biomolecules and keywords. New partners and interactions are added in real time. The process can be repeated iteratively to increase network coverage. Conversely, the user can delete biomolecules and interactions from the network.


MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.

Launay G, Salza R, Multedo D, Thierry-Mieg N, Ricard-Blum S - Nucleic Acids Res. (2014)

Visualization of a network in iNavigator. The navigation bar features a search box. The list of results can be toggled between hits found in MatrixDB or hits found in the displayed network. A button in the top-right corner is used to export the current network or reload a previously saved network. On the left-hand side, buttons provide access to the four main widgets: the tabular network widget, the cart, the network filter widget and a palette widget to change the color of selected nodes. The bottom-right ‘magnifying glass’ widget keeps track of recently visited network elements and allows for the quick inspection of biomolecules and interactions. Hovering the mouse over a node or edge in the network adds that node or edge to the ‘recently visited’ list.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383919&req=5

Figure 3: Visualization of a network in iNavigator. The navigation bar features a search box. The list of results can be toggled between hits found in MatrixDB or hits found in the displayed network. A button in the top-right corner is used to export the current network or reload a previously saved network. On the left-hand side, buttons provide access to the four main widgets: the tabular network widget, the cart, the network filter widget and a palette widget to change the color of selected nodes. The bottom-right ‘magnifying glass’ widget keeps track of recently visited network elements and allows for the quick inspection of biomolecules and interactions. Hovering the mouse over a node or edge in the network adds that node or edge to the ‘recently visited’ list.
Mentions: When browsing MatrixDB, the user can select any publication, biomolecule or UniProtKB keyword and build the corresponding interaction network via iNavigator, a novel interactome network navigator we have developed (Figure 3). The selected items are collected in a cart, which is available on all MatrixDB web pages, and can be deleted from the cart at any time. Interaction networks may be modified either by changing the cart content or by clicking and dragging elements directly on the network. The network can be expanded either by adding the partners and interactions of biomolecules selected within the displayed network, or by querying MatrixDB via the search bar for further publications, biomolecules and keywords. New partners and interactions are added in real time. The process can be repeated iteratively to increase network coverage. Conversely, the user can delete biomolecules and interactions from the network.

Bottom Line: Filters may be applied to build sub-networks based on a list of biomolecules, a specified interaction detection method and/or an expression level by tissue, developmental stage, and health state (UniGene data).Any molecule of the network may be selected and its partners added to the network at any time.Networks may be exported under Cytoscape and tabular formats and as images, and may be saved for subsequent re-use.

View Article: PubMed Central - PubMed

Affiliation: UMR 5086 CNRS - Université Lyon 1, 69367 Lyon Cedex 07, France.

Show MeSH
Related in: MedlinePlus