iDREM

The Dynamic Regulatory Events Miner (DREM) software was initially developed to integrate static protein-DNA interaction data with time series gene expression data for reconstructing dynamic regulatory networks. In recent years, several additional types of high-throughput time series data have been used to study biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Integrating all available time series and static datasets in a unified model remains an important challenge and goal. To address this goal, and to enable interactive queries of the resulting learned models we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and more. Importantly, it also allows users to interactively visualize a gene, TF, path or model-centric view of each of these data types, their interactions and their impact on the resulting model. We showcase the functionality of the new tool by applying it to integrate several data types from multiple labs for modeling microglia development regulatory networks.