Categories
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…
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…
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,…
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…
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…
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. &…
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….
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 …
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…