MatrixDB 2024:增加了细胞外矩阵相互作用的覆盖范围,一个新的网络探索器和一个新的Web接口
Kasun W Samarasinghe1, Max Kotlyar2, Sylvain D Vallet3
1SIB, Swiss Institute of Bioinformatics, Geneva, Switzerland.
Nucleic acids research
|November 18, 2024
概括
MatrixDB是一个对细胞外矩阵 (ECM) 相互作用的升级数据库,现在为研究ECM互动组的研究人员提供了两倍的精选数据和增强的网络分析工具.
科学领域:
- 生物化学 生物化学
- 生物信息学是一种生物信息学.
- 分子生物学分子生物学
背景情况:
- 细胞外基质 (ECM) 对组织结构和功能至关重要.
- 了解ECM组件的相互作用对于生物研究至关重要.
- 现有的数据库可能缺乏全面的,精心策划的ECM交互数据.
研究的目的:
- 为了呈现MatrixDB数据库的升级版本.
- 增强ECM交互的数据可访问性,策划和分析能力.
- 扩大ECM互动组的覆盖范围.
主要方法:
- 数据库架构升级,以改善数据出口,版本管理和程序访问.
- 整合手工策划和实验支持的交互,翻一番以前的内容.
- 从综合交互数据库导入高可信度预测相互作用.
- 标注ECM蛋白与母体组类别以及Reactome通路的添加.
- 通过网络探索器将转录和蛋白质组数据集纳入网络生成.
主要成果:
- 现在MatrixDB包含的手动策划和实验支持的ECM交互的数量超过两倍.
- 通过导入的预测相互作用,扩大了ECM互动组的覆盖范围.
- 增强了对母体体分裂和生物通路的注释.
- 开发一个内部网络探索器,用于生成细胞和组织特定的ECM网络.
结论:
- 升级的MatrixDB为研究ECM相互作用提供了显著增强的资源.
- 改进的数据可访问性和分析工具促进了ECM-omic数据集的计算分析.
- 对于科学界来说,MatrixDB是一个有价值的,免费可用的平台.
更多相关视频
07:28Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis
Published on: July 23, 2015
27.0K
08:32Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo
Published on: May 4, 2018
6.3K
相关概念视频
01:29The Extracellular Matrix
8.9K
Overview
In order to maintain tissue organization, many animal cells are surrounded by structural molecules that make up the extracellular matrix (ECM). Together, the molecules in the ECM maintain the structural integrity of tissue as well as the remarkable specific properties of certain tissues.
Composition of the Extracellular Matrix
The extracellular matrix (ECM) is commonly composed of ground substance, a gel-like fluid, fibrous components, and many structurally and functionally diverse...
In order to maintain tissue organization, many animal cells are surrounded by structural molecules that make up the extracellular matrix (ECM). Together, the molecules in the ECM maintain the structural integrity of tissue as well as the remarkable specific properties of certain tissues.
Composition of the Extracellular Matrix
The extracellular matrix (ECM) is commonly composed of ground substance, a gel-like fluid, fibrous components, and many structurally and functionally diverse...
8.9K
01:24Overview of Cell-Matrix Interactions
7.1K
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...
7.1K
01:26Extracellular Matrix
2.8K
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...
2.8K
01:23Role of Matrix Metalloproteases in Degradation of ECM
2.3K
Matrix metalloproteases (MMPs) are enzymes involved in the hydrolysis of proteins and glycoproteins of the extracellular matrix. MMPs are essential for the migration and proliferation of cells through the dense matrix network, throughout embryonic development, and throughout morphogenesis. The first MMP activity discovered was a collagenase in a tadpole's tail undergoing metamorphosis. The active collagen deposition and modifications lead to the morphogenesis of tadpoles into the adult...
2.3K
01:13Cell-matrix's Response to Mechanical Forces
2.6K
In animal cells, the extracellular matrix allows cells within tissues to withstand external stresses and transmits signals from the outside of the cell to the inside. The extracellular matrix is extensive, and its composition varies between different types of tissues. For example, the reticular fibers and ground substance make up the ECM in loose connective tissue, while collagen and bone minerals make up the ECM of bone tissue.
Anchoring junctions mechanically attach a cell to the...
Anchoring junctions mechanically attach a cell to the...
2.6K