Research ResourceNuclear Receptors

Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine

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Sci. Signal.  25 Apr 2017:
Vol. 10, Issue 476, eaah6275
DOI: 10.1126/scisignal.aah6275

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Data mining to understand nuclear receptor signaling

Transcriptomic data are potentially useful for generating mechanistic hypotheses beyond the original experiment in which they were generated and for independently validating unrelated studies. However, data are often generated and presented in disparate contexts and formats, making it difficult to draw connections between different researchers’ findings. Becnel et al. provide an updated version of Transcriptomine, a data-mining web tool that focuses on nuclear receptor pathway data sets. This tool has been redesigned to be easily used by bench scientists to access and complement data from the published scientific literature. The resource curates more than 500 data sets to allow users to cross-reference information about how different genetic or pharmacological manipulations affect gene expression in different organs or physiological systems and to visualize pathway-gene-tissue relationships. The approach used by the authors can be expanded to other pathways and types of ‘omics data sets.