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NGSmethDB 2017: enhanced methylomes and differential methylation
2016
Nucleic Acids Research
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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). ...
.ugr.es/NGSmethDB 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
2020
Nucleic Acids Research
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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
2016
Nucleic Acids Research
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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]
2017
bioRxiv
pre-print
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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
2015
Open Biology
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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