STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
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DOI：
10.1093/nar/gkv1277
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Kuhn M
中科院分区：
文献类型：
--
作者：
Szklarczyk D;Santos A;von Mering C;Jensen LJ;Bork P;Kuhn M
蛋白质和小分子之间的相互作用是生物体生物过程的一个组成部分。有关这些相互作用的信息分散在许多数据库、文本和预测方法中，这使得很难全面了解现有证据。为了解决这个问题，我们开发了 STITCH（“相互作用化学品搜索工具”），它将 430 000 种化学品的不同数据源集成到一个易于使用的资源中。除了扩大数据库范围之外，我们还实现了新的网络视图，使用户能够查看交互网络中化学品的结合亲和力。这使用户能够快速了解化学品对其相互作用伙伴的潜在影响。对于每个有机体，STITCH 提供了一个全球网络；然而，并非所有蛋白质都具有相同的空间表达模式。因此，只有交互的某个子集可以同时发生。在新的 STITCH 第五版中，我们实现了过滤掉与给定组织无关的蛋白质和化学物质的功能。 STITCH 数据库可以完整下载，通过广泛的 API 以编程方式访问，或者通过重新设计的 Web 界面进行搜索，网址为 http://stitch.embl.de。
Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH (‘Search Tool for Interacting Chemicals’) that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de.