Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways

Abstract

Signaling pathways involving nuclear receptors (NRs), their ligands and coregulators, regulate tissue-specific transcriptomes in diverse processes, including development, metabolism, reproduction, the immune response and neuronal function, as well as in their associated pathologies. The Nuclear Receptor Signaling Atlas (NURSA) is a Consortium focused around a Hub website (www.nursa.org) that annotates and integrates diverse 'omics datasets originating from the published literature and NURSA-funded Data Source Projects (NDSPs). These datasets are then exposed to the scientific community on an Open Access basis through user-friendly data browsing and search interfaces. Here, we describe the redesign of the Hub, version 3.0, to deploy "Web 2.0" technologies and add richer, more diverse content. The Molecule Pages, which aggregate information relevant to NR signaling pathways from myriad external databases, have been enhanced to include resources for basic scientists, such as post-translational modification sites and targeting miRNAs, and for clinicians, such as clinical trials. A portal to NURSA's Open Access, PubMed-indexed journal Nuclear Receptor Signaling has been added to facilitate manuscript submissions. Datasets and information on reagents generated by NDSPs are available, as is information concerning periodic new NDSP funding solicitations. Finally, the new website integrates the Transcriptomine analysis tool, which allows for mining of millions of richly annotated public transcriptomic data points in the field, providing an environment for dataset re-use and citation, bench data validation and hypothesis generation. We anticipate that this new release of the NURSA database will have tangible, long term benefits for both basic and clinical research in this field.

Fig 1. The NURSA 3.0 Homepage.

All data within NURSA are now readily accessible through nine sections within the homepage. Webpages within each NURSA section contain links to pertinent related data within NURSA 3.0, e.g., a Molecule Page will contain links to clinical trials within the Clinical section, and links to external online resources to allow end users to rapidly discover and explore information. Reprinted under a CC BY license, with permission from the Nuclear Receptor Signaling Atlas, original copyright 2015.

Fig 2. The All Molecules Page.

On the All Molecules Page, end users can either browse nuclear receptors, coregulators and ligands, or narrow down the list of molecules using an Amazon-like filter module. In this example, the user enters the GO term “cell death” in the filter module to retrieve molecules mapping to that term. Reprinted under a CC BY license, with permission from the Nuclear Receptor Signaling Atlas, original copyright 2015.

Fig 3. The Molecule Page.

The Molecule Pages aggregate data from numerous external basic and clinical information resources, as well as public and NURSA-funded datasets, reagents and other entities. Reprinted under a CC BY license, with permission from the Nuclear Receptor Signaling Atlas, original copyright 2015.