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

• Published in: The FEBS journal Vol. 291; no. 17; pp. 3938 - 3960
• Main Authors: Maji, Sourobh, Waseem, Mohd, Sharma, Manish Kumar, Singh, Maninder, Singh, Anamika, Dwivedi, Nidhi, Thakur, Pallabi, Cooper, David G, Bisht, Naveen C, Fassler, Jan S, Subbarao, Naidu, Khurana, Jitendra P, Bhavesh, Neel Sarovar, Thakur, Jitendra Kumar
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.09.2024
• Subjects: Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - chemistry; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Baking yeast; Comparative analysis; Computer programs; Databases, Protein; DNA-directed RNA polymerase; Gene expression; Gene regulation; Humans; Mediator Complex - chemistry; Mediator Complex - genetics; Mediator Complex - metabolism; Protein Interaction Mapping; Protein Interaction Maps - genetics; Proteins; RNA polymerase; RNA polymerase II; RNA Polymerase II - chemistry; RNA Polymerase II - genetics; RNA Polymerase II - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Yeast; Yeasts; protein–protein interaction; Mediator complex; transcription; Mediator subunit; network
• ISSN: 1742-464X; 1742-4658; 1742-4658
• DOI: 10.1111/febs.17225

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.