ArticlePhysiological genomics2012
Transcriptomine, a web resource for nuclear receptor signaling transcriptomes.
Article in Physiological genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- Genetic analyses using chromosomal microarray and exome sequencing in fetuses and women with Müllerian duct anomalies.Journal of assisted reproduction and genetics · 2025Article
- Bile acid regulation of xenobiotic nuclear receptors on the expressions of orosomucoids in the liver.American journal of physiology. Endocrinology and metabolism · 2025Article
- Rare variant enrichment analysis supportsHGG advances · 2023Article
- No Dataset Left Behind: Mechanistic Insights into Thyroid Receptor Signaling Through Transcriptomic Consensome Meta-Analysis.Thyroid : official journal of the American Thyroid Association · 2020Article
- The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways.Scientific data · 2019Article
- Sequential gene regulatory events leading to glucocorticoid-evoked apoptosis of CEM human leukemic cells:interactions of MAPK, MYC and glucocorticoid pathways.Molecular and cellular endocrinology · 2018Review
- Transcriptomic response of breast cancer cells to anacardic acid.Scientific reports · 2018Article
- Mutations in GREB1L Cause Bilateral Kidney Agenesis in Humans and Mice.American journal of human genetics · 2017Article
- Growth regulation by estrogen in breast cancer 1 (GREB1) is a novel progesterone-responsive gene required for human endometrial stromal decidualization.Molecular human reproduction · 2017Article
- Improving the discoverability, accessibility, and citability of omics datasets: a case report.Journal of the American Medical Informatics Association : JAMIA · 2017Article
- Editorial: Centennial Celebration - A Focus on Endocrine Disrupting Chemicals… One Hundred Years in the Making.Molecular endocrinology (Baltimore, Md.) · 2016Article
- Research Resource: A Reference Transcriptome for Constitutive Androstane Receptor and Pregnane X Receptor Xenobiotic Signaling.Molecular endocrinology (Baltimore, Md.) · 2016Article
- Autocrine androgen action is essential for Leydig cell maturation and function, and protects against late-onset Leydig cell apoptosis in both mice and men.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2015Article
- Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways.PloS one · 2015Article
- Nuclear Receptor Signaling: a home for nuclear receptor and coregulator signaling research.Nuclear receptor signaling · 2014Review
- The KRAB zinc finger protein RSL1 modulates sex-biased gene expression in liver and adipose tissue to maintain metabolic homeostasis.Molecular and cellular biology · 2014Article
- Article
- Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers.American journal of human genetics · 2013Article
- NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse.Bioinformatics (Oxford, England) · 2013Article
- Minireview: progress and challenges in proteomics data management, sharing, and integration.Molecular endocrinology (Baltimore, Md.) · 2012Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
The nuclear receptor (NR) superfamily of ligand-regulated transcription factors directs ligand- and tissue-specific transcriptomes in myriad developmental, metabolic, immunological, and reproductive processes. The NR signaling field has generated a wealth of genome-wide expression data points, but due to deficits in their accessibility, annotation, and integration, the full potential of these studies has not yet been realized. We searched public gene expression databases and MEDLINE for global transcriptomic datasets relevant to NRs, their ligands, and coregulators. We carried out extensive, deep reannotation of the datasets using controlled vocabularies for RNA Source and regulating molecule and resolved disparate gene identifiers to official gene symbols to facilitate comparison of fold changes and their significance across multiple datasets. We assembled these data points into a database, Transcriptomine (http://www.nursa.org/transcriptomine), that allows for multiple, menu-driven querying strategies of this transcriptomic "superdataset," including single and multiple genes, Gene Ontology terms, disease terms, and uploaded custom gene lists. Experimental variables such as regulating molecule, RNA Source, as well as fold-change and P value cutoff values can be modified, and full data records can be either browsed or downloaded for downstream analysis. We demonstrate the utility of Transcriptomine as a hypothesis generation and validation tool using in silico and experimental use cases. Our resource empowers users to instantly and routinely mine the collective biology of millions of previously disparate transcriptomic data points. By incorporating future transcriptome-wide datasets in the NR signaling field, we anticipate Transcriptomine developing into a powerful resource for the NR- and other signal transduction research communities.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.