ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database

Zhitao Mao, Ruoyu Wang, Haoran Li, Yixin Huang, Qiang Zhang, Xiaoping Liao, Hongwu Ma
2022 Nucleic Acids Research  
Cellular regulation is inherently complex, and one particular cellular function is often controlled by a cascade of different types of regulatory interactions. For example, the activity of a transcription factor (TF), which regulates the expression level of downstream genes through transcriptional regulation, can be regulated by small molecules through compound–protein interactions. To identify such complex regulatory cascades, traditional relational databases require ineffective additional
more » ... ations and are computationally expensive. In contrast, graph databases are purposefully developed to execute such deep searches efficiently. Here, we present ERMer (E. coli Regulation Miner), the first cloud platform for mining the regulatory landscape of Escherichia coli based on graph databases. Combining the AWS Neptune graph database, AWS lambda function, and G6 graph visualization engine enables quick search and visualization of complex regulatory cascades/patterns. Users can also interactively navigate the E. coli regulatory landscape through ERMer. Furthermore, a Q&A module is included to showcase the power of graph databases in answering complex biological questions through simple queries. The backend graph model can be easily extended as new data become available. In addition, the framework implemented in ERMer can be easily migrated to other applications or organisms. ERMer is available at https://ermer.biodesign.ac.cn/.
doi:10.1093/nar/gkac288 pmid:35489073 pmcid:PMC9252789 fatcat:34axbrde45fzjeqvh2cbidcz6y