CisBP and CisBP-RNA: web resources for protein-DNA and protein-RNA binding models

Project Summary and Abstract The processes underlying human health and disease are highly complex. This necessitates the creation, organization, and dissemination of vast amounts of relevant scientific data. Organizing this information into databases and user-friendly web sites and tools is therefore an integral component of ongoing efforts to understand and ultimately improve human health. Many human diseases are now appreciated to result from genetic and environmental perturbations to gene regulatory mechanisms. As direct readers of genomic regulatory sequences, transcription factors (TFs) and RNA-binding proteins (RBPs) are primary components of gene regulatory mechanisms. Accordingly, the nucleic acid binding specificities of TFs and RBPs (henceforth, “specificities”) provide foundational knowledge for understanding the processes underlying human health and disease states. Comprehensive mapping of TF and RBP specificities is thus regarded as a major goal in the fields of human genetics, functional genomics, and bioinformatics. We aim to ultimately achieve this goal and disseminate the resulting data freely to the research community. To this end, we created the CisBP and CisBP-RNA TF and RBP specificity databases over 10 years ago. Since then, we have improved upon these resources through periodic updates incorporating new experimental data generated in our labs and others. Since their creation, these unique resources have been heavily utilized by the research community, with over 60,000 unique users and over 2,800 citations to date. Our ongoing efforts to maintain and improve CisBP and CisBP-RNA have enabled the comprehensive study of gene regulation in healthy and disease states in humans and other organisms relevant to human health. In this proposal, we seek to build upon these powerful resources by improving the database contents and underlying computational infrastructure (Aim 1), incorporating newly generated specificity data for TFs and RBPs from human viruses and other important human pathogens (Aim 2), and enhancing the user experience through improved web sites, web tools, and community outreach efforts (Aim 3). Implementation of these improvements will directly lead to increased database update frequencies, improved user experiences, a large and more knowledgeable user community, and new data for studying the role of gene regulation in human healthy and disease states.