Analysis of the dexamethasone (Dex)-regulated transcriptome in lipopolysaccharide (LPS)-activated inflammatory mouse macrophages

Yu, RT

doi:10.1621/njyedq96t7

Signaling Pathways Project Datasets

DOI: 10.1621/njyedq96t7

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Analysis of the dexamethasone (Dex)-regulated transcriptome in lipopolysaccharide (LPS)-activated inflammatory mouse macrophages

RT Yu¹

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“…SERP1 in LNCaP cells(54)(55)(56)(57) and mouse testis(46,47)], by the GR and glucocorticoids pathway [HSPA5 in mouse liver(58,59) and rat kidney(60,61) and SERP1 in mouse bone marrow-derived macrophages(62,63) and human HLE B-3 cells(64, 65)], and by the PPARs and fatty acids pathway [XBP1 during 3T3-L1 adipogenesis (66, 67)]. Use Case 2 focuses on the utility of Transcriptomine Animal and Cell Model experiments in building confidence in a hypothesis previously uncharacterized in the research literature, for the role of two distinct NR signaling pathways in the regulation of 3T3-L1 adipogenesis.…”

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

et al. 2017

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We previously developed a web tool, Transcriptomine, to explore expression profiling data sets involving small-molecule or genetic manipulations of nuclear receptor signaling pathways. We describe advances in biocuration, query interface design, and data visualization that enhance the discovery of uncharacterized biology in these pathways using this tool. Transcriptomine currently contains about 45 million data points encompassing more than 2000 experiments in a reference library of nearly 550 data sets retrieved from public archives and systematically curated. To make the underlying data points more accessible to bench biologists, we classified experimental small molecules and gene manipulations into signaling pathways and experimental tissues and cell lines into physiological systems and organs. Incorporation of these mappings into Transcriptomine enables the user to readily evaluate tissue-specific regulation of gene expression by nuclear receptor signaling pathways. Data points from animal and cell model experiments and from clinical data sets elucidate the roles of nuclear receptor pathways in gene expression events accompanying various normal and pathological cellular processes. In addition, data sets targeting non-nuclear receptor signaling pathways highlight transcriptional cross-talk between nuclear receptors and other signaling pathways. We demonstrate with specific examples how data points that exist in isolation in individual data sets validate each other when connected and made accessible to the user in a single interface. In summary, Transcriptomine allows bench biologists to routinely develop research hypotheses, validate experimental data, or model relationships between signaling pathways, genes, and tissues.

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confidence: 99%

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

et al. 2017

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Analysis of the dexamethasone (Dex)-regulated transcriptome in lipopolysaccharide (LPS)-activated inflammatory mouse macrophages

Cited by 1 publication

References 0 publications

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

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

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