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161.
Gottesfeld JM Belitsky JM Melander C Dervan PB Luger K 《Journal of molecular biology》2002,321(2):249-263
162.
Sheng Li Francine Garrett-Bakelman Alexander E Perl Selina M Luger Chao Zhang Bik L To Ian D Lewis Anna L Brown Richard J D’Andrea M Elizabeth Ross Ross Levine Martin Carroll Ari Melnick Christopher E Mason 《Genome biology》2014,15(9)
We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation sequencing data. We quantify the changes using a composition entropy difference calculation and also introduce a new measure of global clonality shift, loci with epiallele shift per million loci covered, which enables comparisons between different samples to gauge overall epiallelic dynamics. Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0472-5) contains supplementary material, which is available to authorized users. 相似文献163.
A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin 总被引:3,自引:0,他引:3 下载免费PDF全文
164.
Hashem?A?Shihab Julian?Gough Matthew?Mort David?N?Cooper Ian?NM?Day Tom?R?GauntEmail author 《Human genomics》2014,8(1):11
As the number of non-synonymous single nucleotide polymorphisms (nsSNPs) identified through whole-exome/whole-genome sequencing programs increases, researchers and clinicians are becoming increasingly reliant upon computational prediction algorithms designed to prioritize potential functional variants for further study. A large proportion of existing prediction algorithms are ‘disease agnostic’ but are nevertheless quite capable of predicting when a mutation is likely to be deleterious. However, most clinical and research applications of these algorithms relate to specific diseases and would therefore benefit from an approach that discriminates between functional variants specifically related to that disease from those which are not. In a whole-exome/whole-genome sequencing context, such an approach could substantially reduce the number of false positive candidate mutations. Here, we test this postulate by incorporating a disease-specific weighting scheme into the Functional Analysis through Hidden Markov Models (FATHMM) algorithm. When compared to traditional prediction algorithms, we observed an overall reduction in the number of false positives identified using a disease-specific approach to functional prediction across 17 distinct disease concepts/categories. Our results illustrate the potential benefits of making disease-specific predictions when prioritizing candidate variants in relation to specific diseases. A web-based implementation of our algorithm is available at http://fathmm.biocompute.org.uk. 相似文献
165.
Dmitri Shinder Dror Luger Mark Rusal Victor Rzepakovsky Valentina Bresler Shlomo Yahav 《Journal of thermal biology》2002,27(6):57-523
The influence of short repetitive cold exposure at an early age (cold conditioning—exposure to 15°C for 3 h at 3 and 4 days of age) on chickens’ thermotolerance during cold challenge (15°C) at 21 days of age was examined. The first cold exposure elicited a dramatic decline in body temperature (Tb) and a significant elevation in stress response (plasma corticosterone concentration); the second cold exposure resulted in moderate Tb and stress responses. Thereafter, the corticosterone concentration remained at a significantly lower level. Acute cold challenge of conditioned broilers at 21 days of age revealed better Tb and stress recovery during the first 24 h, and a significantly lower mortality rate thereafter. Conditioned chickens exposed to optimal conditions (22°C) achieved significantly higher body weights than others. It may be concluded that early cold conditioning improves thermotolerance in broiler chickens in later life. 相似文献
166.
Structure and function of nucleosome assembly proteins. 总被引:1,自引:0,他引:1
167.
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169.
Although 2,3,4-tri-O-acetyl-β-D-xylopyranosyl chloride is shown by n.m.r. data to be 80 percent in the 1C4 conformation in chloroform solution, it crystallizes in the normal 4C1 conformation as shown by a three-dimensional, X-ray structure analysis. The crystals are orthorhombic, space group P212121. The phase problem was solved by the heavy-atom method. The parameters were refined to an R-value of 0.039 for 1101 structure factors. With the chlorine atom being in equatorial position in the 4C1 conformation, the C-1O-6 bond is not shortened and the C-1Cl-1 bond is not lengthened. These results are in agreement with comparable values for cis-2,3-dichloro-1,4-dioxane. 相似文献
170.
Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF