MediatorWeb: a protein–protein interaction network database for the RNA polymerase II Mediator complex

Sourobh Maji, Mohd Waseem, Manish Kumar Sharma, Maninder Singh, Anamika Singh, Nidhi Dwivedi, Pallabi Thakur, David G. Cooper, Naveen C. Bisht, Jan S. Fassler, Naidu Subbarao, Jitendra P. Khurana, Neel Sarovar Bhavesh, Jitendra Kumar Thakur
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Abstract

The protein–protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user-friendly web-interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue–level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.

Abstract Image

MediatorWeb:RNA 聚合酶 II Mediator 复合物的蛋白质-蛋白质相互作用网络数据库。
介体复合体的蛋白质-蛋白质相互作用(PPI)网络受到非常严格的调控,并取决于不同的发育和环境线索。在这里,我们在一个名为 MediatorWeb 的用户友好型网络界面数据库中提供了一个互动平台,用于比较分析来自人类、面包酵母和模式植物拟南芥的 Mediator 亚基。MediatorWeb 提供了一个可视化和分析 Mediator 亚基 PPI 网络的界面。该数据库便于下载 Mediator 复合物、其子模块和单个 Mediator 亚基的非目标和非加权网络,从而更好地直观显示单个 Mediator 亚基或其子模块的重要性。此外,MediatorWeb 还提供 Mediator 复合物和有功能注释的相互作用蛋白的网络可视化。这一功能为了解 Mediator 亚基在不同过程中的功能提供了线索。在另一个选项卡中,MediatorWeb 提供了二级和三级结构的快速访问,以及三种模式生物中每个 Mediator 亚基的残基级联系信息。MediatorWeb 的另一个有用功能是根据同源物分析检测同源物,这可以为了解 Mediator 复合物在探索较少的生物界中的功能提供线索。因此,MediatorWeb 及其功能可以帮助用户了解 Mediator 复合物及其亚基在基因表达转录调控中的作用。
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