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Extracellular Matrix01:26

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Unlike epithelial tissue, which is composed of cells closely packed with little or no extracellular space in between, connective tissue cells are dispersed in a matrix. This extracellular matrix (ECM) is composed of fibrous proteins like collagen, elastin, and fibronectin in a ground substance consisting of interstitial fluid, cell adhesion proteins, and proteoglycans. The proteoglycans form a gel-like material in the spaces between cells and provide hydration, buffering, binding, and force...
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The extracellular matrix or ECM holds cells together to form a tissue and allows the cells within the tissue to communicate. ECM comprises proteins such as fibronectin, collagen, laminin, etc. The most abundant protein in this space is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. ECM allows cell migration and provides a structural scaffold at cell adhesion that anchors the cell when the extracellular matrix proteins interact with...
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Fibronectin is an adhesive glycoprotein present in the extracellular matrix of embryogenic and adult tissue. These molecules primarily aid in regulating cell motility and attachment. A fibronectin molecule is composed of two identical polypeptide chains attached to each other by a pair of disulfide bonds at the C-terminal.
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MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded

G Launay1, R Salza1, D Multedo1

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

Nucleic Acids Research
|November 8, 2014
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Summary
This summary is machine-generated.

MatrixDB is a database for extracellular protein and polysaccharide interactions, updated with new features like iNavigator for network visualization and filtering. It facilitates the exploration and export of complex biological interaction networks.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Molecular Biology

Background:

  • Extracellular proteins and polysaccharides play crucial roles in cellular processes.
  • Understanding their interactions is vital for deciphering complex biological pathways.
  • Existing databases may lack comprehensive or specialized data on these interactions.

Purpose of the Study:

  • To present MatrixDB, a freely available database dedicated to extracellular molecular interactions.
  • To highlight recent updates including a new website and an advanced network visualization tool.
  • To provide enhanced capabilities for analyzing and exporting interaction data.

Main Methods:

  • Curation of interaction data and import from other International Molecular Exchange (IMEx) consortium databases.
  • Adoption of Proteomics Standards Initiative Molecular Interaction (PSI-MI) standards for data annotation.
  • Development of iNavigator, a graphical tool for building and exploring interaction networks with advanced filtering options.

Main Results:

  • MatrixDB offers curated and imported data on extracellular protein and polysaccharide interactions.
  • The new iNavigator tool allows users to construct and visualize complex interaction networks.
  • Users can filter networks by biomolecule, interaction detection method, and expression data across tissues and developmental stages.
  • Networks can be exported in various formats (Cytoscape, tabular, images) and saved for future use.

Conclusions:

  • MatrixDB serves as a valuable, updated resource for researchers studying extracellular interactions.
  • The enhanced visualization and filtering tools facilitate in-depth network analysis.
  • The database supports data sharing and integration through adherence to IMEx standards.