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NGSmethDB 2017: enhanced methylomes and differential methylation

Ricardo Lebrón, Cristina Gómez-Martín, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Michael Hackenberg, José L. Oliver
2016 Nucleic Acids Research  
The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology.  ...  methylated single-cytosines; and (ii) methylation segments (i.e. genome regions of homogeneous methylation).  ... API/ NGSmethDB API.ova), described in this paper, which allow downloading all the NGSmethDB data (singlecytosine methylation, methylation segments and differentially methylated cytosines  ... 
doi:10.1093/nar/gkw996 pmid:27794041 pmcid:PMC5210667 fatcat:qa55agoltjgljh6bhotxum5sd4

MethHC 2.0: information repository of DNA methylation and gene expression in human cancer

Hsi-Yuan Huang, Jing Li, Yun Tang, Yi-Xian Huang, Yi-Gang Chen, Yue-Yang Xie, Zhe-Yuan Zhou, Xin-Yi Chen, Si-Yuan Ding, Meng-Fan Luo, Chen-Nan Jin, Le-Shan Zhao (+9 others)
2020 Nucleic Acids Research  
Provided features include clinical-pathological data, mutation and copy number variation, multiplicity of information (gene regions, enhancer regions, and CGI regions), and circulating tumor DNA methylation  ...  DNA methylation is an important epigenetic regulator in gene expression and has several roles in cancer and disease progression.  ...  into the updated NGSMethDB 2017 (21, 22) .  ... 
doi:10.1093/nar/gkaa1104 pmid:33270889 fatcat:2ndovmo4szaa3h5tpi2fodk65m

DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database

Yichun Xiong, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, Jiang Zhu, Yihan Wang, Hongbo Liu, Yan Zhang
2016 Nucleic Acids Research  
In particular, we enhanced the differential analysis tools, which now enable online automated identification of DNA methylation abnormalities in human disease in a case-control or disease-disease manner  ...  To facilitate further mining of the disease methylome, three new web tools were developed for cluster analysis, functional annotation and survival analysis.  ...  ACKNOWLEDGEMENTS We thank TCGA, GEO, the NIH Roadmap Epigenomics, ENCODE and other projects for generating and sharing the data used in this paper.  ... 
doi:10.1093/nar/gkw1123 pmid:27899673 pmcid:PMC5210584 fatcat:kyydehv52jdfdm3ie23adwemfa

Euplotid: A quantized geometric model of the eukaryotic cell [article]

Diego Borges-Rivera
2017 bioRxiv   pre-print
Reads are quantified using the latest computational tools and the results are normalized, quality-checked, and stored.  ...  Euplotid is composed of a set of quantized geometric 3D building blocks and constantly evolving bioinformatic pipelines encapsulated and running in Docker containers enabling a user to build and annotate  ...  loaded Acetylation of H3 at Super Enhancers [37] .  ... 
doi:10.1101/170159 fatcat:ehzqifporrexbnnezrd24l4ygq

MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes

Shi Wang, Jia Lv, Lingling Zhang, Jinzhuang Dou, Yan Sun, Xue Li, Xiaoteng Fu, Huaiqian Dou, Junxia Mao, Xiaoli Hu, Zhenmin Bao
2015 Open Biology  
Open Biol. 5: 150130. http://dx.Characterization of dynamic DNA methylomes in diverse phylogenetic groups has attracted growing interest for a better understanding of the evolution of DNA methylation as  ...  Research Cite this article: Wang S et al. 2015 MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes.  ...  We thank Dr Fengning Xiang (Shandong University) for providing some A. thaliana seed samples and Zhangzidao Fishery Group Co. for assistance with scallop sampling.  ... 
doi:10.1098/rsob.150130 pmid:26581575 pmcid:PMC4680569 fatcat:viqmu3moobcbhavroxa2xhgllq