Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms.
Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms.
复制标题
DOI：
10.1242/jcs.261255
复制
发表时间：
2023-09-01
影响因子：
4
通讯作者：
中科院分区：
文献类型：
--
作者：
细胞外基质（ECM）是一种复杂的蛋白质网络，形成多细胞生物体中所有组织的支架。它在生命的各个方面都起着至关重要的作用-从在发育过程中协调细胞迁移到支持组织修复。它在疾病的病因学或进展中也起着关键作用。为了研究这个区室，我们先前已经定义了多种生物体的ECM和ECM相关蛋白的所有编码基因的概要。我们将这种纲要称为“基质体”，并将基质体组分进一步分类为不同的结构或功能类别。这种命名法现在主要被研究界采用来注释“组学”数据集，并有助于推进基础和翻译ECM研究。在这里，我们报告了Matrisome AnalyzeR的开发，这是一套工具，包括一个基于Web的应用程序和一个R包。该Web应用程序可供任何对大型数据集中的基质体分子进行注释、分类和制表感兴趣的人使用，而无需编程知识。配套的R包可供更有经验的用户使用，对处理更大的数据集或其他数据可视化选项感兴趣。总结：Matrisome AnalyzeR是一套工具，包括一个基于Web的应用程序和一个R包，旨在促进大数据集中细胞外基质成分的注释和定量。
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays crucial roles in all aspects of life – from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we have previously defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the ‘matrisome’ and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate ‘-omics’ datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application and an R package. The web application can be used by anyone interested in annotating, classifying and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options. Summary: Matrisome AnalyzeR is a suite of tools, including a web-based app and an R package, designed to facilitate the annotation and quantification of extracellular matrix components in big datasets.