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Norway

dkNET Data Archive: NURSA (Nuclear Receptor Signaling Atlas)   

Nuclear Receptor Signaling Atlas (NURSA)

Nuclear Receptor Signaling Atlas (NURSA) is a software tool as a knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. NURSA includes large validated data sets (transcriptomic and non-transcriptomic), molecular pages, access to reagents such as antibodies, cell lines, PCR primers, and mouse models, and a tool "Transcriptomine" used for discovering relationships between nuclear receptor signaling pathways, genes and tissues.

NURSA was supported by NIDDK for 15 years. As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP), an integrated transcriptomic/ChIP-seq knowledgebase for mammalian cellular signaling pathways. An article on SPP was published in Nature Scientific Data. All NURSA-biocurated transcriptomic datasets have been preserved for data mining in SPP. All non-transcriptomic dataset NURSA content will be transferred to dkNET. dkNET team is evaluating options for archiving this content. dkNET also houses all other curated information on animal models, antibodies, cell lines, molecules, and PCR primers.


Access NURSA Data

Datasets

Molecules

Transcriptomic Dataset
All NURSA-biocurated transcriptomic datasets have been preserved for data mining in SPP through an enhanced and expanded version of Transcriptomine named Ominer. To access these datasets, dkNET provides users with the information of 527 transcriptomic datasets that contain data related to nuclear receptors and nuclear receptor coregulators in the NURSA Datasets table view and redirects users to the current SPP dataset page. Once users find the specific dataset of research interest, users can download the dataset by clicking DOI and then clicking the Download Dataset button at the SPP webpage.
Non-Transcriptomic Dataset
All NURSA-biocurated non-transcriptomic dataset NURSA content will be transferred to dkNET. The dkNET team is evaluating options for archiving this content. Currently, users can get access to the metadata of these 21 datasets through dkNET's NURSA Datasets table view. The DOI is currently unlinked, but will be relinked once the dataset landing page is preserved completely.
Molecules
Users can get access to the NURSA-biocurated molecules metadata through dkNET's NURSA Molecules table view. Users can refine the data by selecting the molecule type of your research interest (nuclear receptors, ligands, or coregulators) from the facet on the left side, searching the data from the top search bar or by clicking the name of the column title firstly and searching under each column. PubChem ID and ChEBI ID information will be available in the future. Additional information, such as Gene, RNA, Protein, GO Terms, Post-Translational Modifications, Crystal Structures, Protein-Protein Interactions, and Targeting miRNAs, shown at the NURSA molecular page which was aggregated from public data repositories, is not currently archived.

Reagents

Animal Models
Users can get access to the NURSA-biocurated animal models metadata through dkNET's NURSA Animal Models table view.
Antibodies
Users can get access to the NURSA-biocurated antibodies metadata through dkNET's NURSA Antibodies table view.
Cell lines
Users can get access to the NURSA-biocurated cell lines metadata through dkNET's NURSA Cell lines table view.
PCR Primers
Users can get access to the NURSA-biocurated PCR primers metadata through dkNET's NURSA PCR Primers table view.

Tool

Transcriptomine
The SPP query interface, Ominer, is the enhanced and expanded version of Transcriptomine. SPP is a foundation for the Hypothesis Center within dkNET. Ominer allows a user to specify a single gene target, Gene Ontology (GO) term or custom gene list and to dial in additional node and biosample regulatory parameters. Detailed information about Ominer and a step-by-step user interface tutorial can be accessed in the SPP paper published in Nature Scientific Data.
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