0000000000951795
AUTHOR
Moritz Hess
Additional file 9 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 9: Web Table 1B. Differentially expressed genes 4 h after exposure to low dose ionizing radiation (0.05 Gray).
Additional file 10 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 10: Web Table 1C. Differentially expressed genes 2 h after exposure to high dose ionizing radiation (2 Gray).
Additional file 8 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 8: Web Table 1A. Differentially expressed genes 2 h after exposure to low dose ionizing radiation (0.05 Gray).
Hepatic B cell leukemia-3 promotes hepatic steatosis and inflammation through insulin-sensitive metabolic transcription factors.
Background & Aims The pathomechanisms underlying non-alcoholic fatty liver disease (NAFLD) and the involved molecular regulators are incompletely explored. The nuclear factor-kappa B (NF-κB)-cofactor gene B cell leukemia-3 ( Bcl-3 ) plays a critical role in altering the transcriptional capacity of NF-κB – a key inducer of inflammation – but also of genes involved in cellular energy metabolism. Methods To define the role of Bcl-3 in non-alcoholic steatohepatitis (NASH), we developed a novel transgenic mouse model with hepatocyte-specific overexpression of Bcl-3 ( Bcl-3 Hep ) and employed a high-fat, high-carbohydrate dietary feeding model. To characterize the transgenic model, deep RNA seque…
Additional file 2 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 2: Web Figure 7. Shared pathways from low and high dose ionizing radiation experiments. Gy = Gray. Web Figure 8. Pathways only affected in high dose ionizing radiation experiments. Gy = Gray.
Additional file 3 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 3: Web Figure 9. Predicted downsteam diseases and functions. Web Figure 10. Predicted upstream regulators. LDIR = Low dose of ionizing radiation (0.05 Gray), HDIR = High dose of ionizing radiation (2 Gray).
Genetic variants linked to myopic macular degeneration in persons with high myopia: CREAM Consortium.
Purpose: To evaluate the roles of known myopia-associated genetic variants for development of myopic macular degeneration (MMD) in individuals with high myopia (HM), using case-control studies from the Consortium of Refractive Error and Myopia (CREAM). Methods: A candidate gene approach tested 50 myopia-associated loci for association with HM and MMD, using meta-analyses of case-control studies comprising subjects of European and Asian ancestry aged 30 to 80 years from 10 studies. Fifty loci with the strongest associations with myopia were chosen from a previous published GWAS study. Highly myopic (spherical equivalent [SE] ≤ -5.0 diopters [D]) cases with MMD (N = 348), and two sets of cont…
Additional file 1 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 1: Web Figure 1. Representative measurements of the cell cycle distribution of HOECHST33258-stained fibroblasts by flow cytometry during (A) log-phase growth or (B) after G0/1 synchronization over 14 days for radiation experiments. Web Figure 2. Total number of differentially expressed genes in human fibroblasts from cancer free-controls at 0.25 h, 2 h and 24 h after exposure to low (0.05 Gray (Gy)) or high dose (2Gy) of X-rays compared to unirradiated fibroblasts (N = 3). Web Figure 3. Correlation of RNA quality metrics (RIN, Qbit RNA-concentration), expression variation (PC1–3) and number of aligned reads (aligned reads, aligned reads normalized) for all experiments. The c…
Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Abstract Background Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points. Methods Fibroblasts from skin biopsies of…
Partitioned learning of deep Boltzmann machines for SNP data.
Abstract Motivation Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. Results After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen…
A genome-wide association study of corneal astigmatism: The CREAM Consortium
Contains fulltext : 191261.pdf (Publisher’s version ) (Open Access) Purpose: To identify genes and genetic markers associated with corneal astigmatism. Methods: A meta-analysis of genome-wide association studies (GWASs) of corneal astigmatism undertaken for 14 European ancestry (n=22,250) and 8 Asian ancestry (n=9,120) cohorts was performed by the Consortium for Refractive Error and Myopia. Cases were defined as having >0.75 diopters of corneal astigmatism. Subsequent gene-based and gene-set analyses of the meta-analyzed results of European ancestry cohorts were performed using VEGAS2 and MAGMA software. Additionally, estimates of single nucleotide polymorphism (SNP)-based heritability for …
Additional file 5 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 5: Web Figure 12. Comparison of predicted downstream diseases and functions in different data sets.
Additional file 6 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 6: Web Figure 13. Comparison of predicted upstream regulators in different data sets.
Additional file 7 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 7: Gene expression in the "Not a Number" pathways (blue = downregulation, red = upregulation). Web Figure 14. Base excision repair (BER) system. Web Fig. 15. Molecular mechanisms of cancer. Web Fig. 16. Assembly of RNA polymerase III complex. Web Fig. 17. DNA double-strand break repair by homologous recombination. Web Fig. 18. Interleukin 4 (IL-4) signaling. Web Fig. 19. Interleukin 17 (IL-17) signaling. Web Fig. 20. Interleukin 17A (IL-17A) signaling in fibroblasts. Web Fig. 21. Mitochondrial dysfunction. Web Fig. 22. Myc mediated apoptosis signaling. Web Fig. 23.Nucleotide excision repair. Web Fig. 24. Protein ubiquitination. Web Fig. 25. Retinoic acid receptor (RAR) activ…
Additional file 4 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 4: Web Figure 11. Comparison of affected pathways in different data sets.
Additional file 11 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 11: Web Table 1D. Differentially expressed genes 4 h after exposure to high dose ionizing radiation (2 Gray).
Additional file 12 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 12: Web Table 2. Differential expression activity in cellular pathways and involved molecules
Additional file 13 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation
Additional file 13: Supplement file 1. Settings for comparison analyses in IPA.