ArticleNature biotechnology2013
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.
Article in Nature biotechnology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Bridging the variant-to-function gap in type 2 diabetes: advances and challenges.Diabetologia · 2026Review
- Insights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity.Scientific reports · 2024Article
- Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure.Nature communications · 2022Article
- Leveraging the cell lineage to predict cell-type specificity of regulatory variation from bulk genomics.Genetics · 2021Article
- Cell Type- and Stimulation-Dependent Transcriptional Programs Regulated by Atg16L1 and Its Crohn's Disease Risk Variant T300A.Journal of immunology (Baltimore, Md. : 1950) · 2020Article
- Combining Multiple Approaches and Models to Dissect the Genetic Architecture of Resistance to Infections in Fish.Frontiers in genetics · 2020Review
- Klotho: A Major Shareholder in Vascular Aging Enterprises.International journal of molecular sciences · 2019Review
- Klotho: An Elephant in Aging Research.The journals of gerontology. Series A, Biological sciences and medical sciences · 2019Review
- Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling.International journal of molecular sciences · 2019Article
- Article
- Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus).BMC genomics · 2018Article
- Article
- Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations.Nature communications · 2017Article
- Article
- Writ large: Genomic dissection of the effect of cellular environment on immune response.Science (New York, N.Y.) · 2016Review
- Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin.PLoS genetics · 2016Article
- POEM: Identifying Joint Additive Effects on Regulatory Circuits.Frontiers in genetics · 2016Article
- Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.Cell reports · 2015Article
- A statistical framework for revealing signaling pathways perturbed by DNA variants.Nucleic acids research · 2015Article
- Genetic basis of autoimmunity.The Journal of clinical investigation · 2015Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.
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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.