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

Abstract

MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. It is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data, either at the MIMIx or IMEx level. MatrixDB content has been updated by curation and by importing extracellular interaction data from other IMEx databases. Other major changes include the creation of a new website and the development of a novel graphical navigator, iNavigator, to build and expand interaction networks. 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.

Figure 1.

(A) The biomolecule report page: biomolecule data. The top bar allows to quickly scroll to the various subsections of the report page. Biomolecule-specific information is shown as boxes. When their 3D structures are available, they can be rotated. (B) The biomolecule report page: interaction data. The biomolecule's ECM partners stored in MatrixDB are listed, along with the number of individual experiments that support each interaction. Clicking on such a number pops up a window listing the experiments and linking to their report pages. The counts and experiments are colored green when involving the molecule itself, and orange when a homolog from another species was used in the experiment. Additional partners found in other cellular compartments can be identifed through the PSICQUIC remote-query widget. The number of items currently in the cart is displayed at the top, and provides a direct access to iNavigator (network icon).

Figure 2.

The experiment report page. As in the biomolecule report page, the top bar allows to scroll to subsections, displays the current cart size and provides direct access to iNavigator. The gray box displays information about the experiment (interaction type, detection method, external references and supporting information). When available, kinetics and affinity data are also shown. Specific information concerning each partner is presented below in blue boxes (e.g. binding sites, biochemical modifications and mutations).

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.

Figure 4.

The network filter widget. The widget displays two filters: ‘expression level’ (in transcripts per million) for biomolecules, and ‘detection method’ for interactions. Checking several boxes imposes all criteria to be met (i.e. logical AND). An expression level (TPM) threshold can be specified, and applies to all selected tissues/health state/developmental stages. The widget uses a color code to preview the effect of a filter on network elements: green elements meet the criteria while red ones do not. Biomolecules that lack expression data are colored in cyan and called Missing Data Elements (MDE). They can be excluded from the network by unchecking the MDE box, hence appearing in red. Clicking on the apply button will hide all the red elements.