Tag: REVIGO

Genetic risk converges on regulatory networks mediating early type 2 diabetes

Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article  ADS  PubMed  Google Scholar  Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…

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Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

A supply of nitrate triggers organ-specific changes of histone modifications at specific gene loci To investigate the organ specificity of dynamic histone modifications in response to N changes, we treated 3-week-old tomato seedlings (Solanum lycopersicum, cultivar M82) with four days of N starvation, followed by N-supply (2.8 mM NO3−; +N) or…

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Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish

Krause, J. & Ruxton, G. D. Living in Groups (Oxford Univ. Press, 2002). Réale, D., Reader, S. M., Sol, D., McDougall, P. T. & Dingemanse, N. J. Integrating animal temperament within ecology and evolution. Biol. Rev. 82, 291–318 (2007). Article  PubMed  Google Scholar  Gartland, L. A., Firth, J. A., Laskowski,…

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rrvgo

rrvgo 1 Hi, this is a long shot, but my own reading and attempts and ChatGPT have all failed me. The REVIGO webapp produces some great graphs of reduced GO terms. You can largely reproduce this in R standalone with the bioconductor rrvgo package. However, the webapp graphs allow filtering…

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Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population | BMC Genomics

Oikonomou EK, Antoniades C. The role of adipose tissue in cardiovascular health and disease. Nat Rev Cardiol. 2019;16(2):83–99. Article  PubMed  Google Scholar  Sakers A, De Siqueira MK, Seale P, Villanueva CJ. Adipose-tissue plasticity in health and disease. Cell. 2022;185(3):419–46. Article  CAS  PubMed  Google Scholar  Sun W, von Meyenn F, Peleg-Raibstein…

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The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Billings, W. Adaptations and origins of alpine plants. Arct. Alp. Res. 6, 129–142 (1974). Article  Google Scholar  Agakhanjanz, O. & Breckle, W. Origin and evolution of the mountain flora in middle Asia and neighbouring mountain regions. in Arctic and Apine Biodiversity: Patterns, Causes and Ecosystem Consequences (eds. Chapin, F. &…

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Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

Conway Morris, S. The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften 96, 1313–1337 (2009). Article  ADS  CAS  PubMed  Google Scholar  Stern, D. L. The genetic causes of convergent evolution. Nat. Rev. Genet. 14, 751–764 (2013). Article  CAS  PubMed  Google Scholar  Christiansen, K. Convergence and parallelism in cave entomobryinae….

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Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes

Litman, G. W., Cannon, J. P. & Dishaw, L. J. Reconstructing immune phylogeny: New perspectives. Nat. Rev. Immunol. 5, 866–879 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  Criscitiello, M. F. & de Figueiredo, P. Fifty shades of immune defense. Heitman J, editor. PLoS Pathog. 9, e1003110 (2013). Article  CAS …

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Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing

Method overview For all presentations, we call the genetic effects on GWAS phenotypes ‘phenotypic effects’ and the effect of gene expression the ‘eQTL effect’. TWAS was originally developed to integrate eQTL and GWAS datasets derived from matched ancestries5. Specifically, it first builds gene expression prediction models using eQTL datasets that…

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