Tag: DMR

DOI: 10.18129/B9.bioc.REMP     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see REMP. Repetitive Element Methylation Prediction Bioconductor version: 3.13 Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide…

Genome-wide DNA methylation changes occur early in human lung fibroblasts during COPD and progress with disease development. A. Lung function data of COPD (II-IV) and no COPD (ex-smoker controls) donors used in this study. The lung function between the two groups is significantly different. B. Schematic diagram illustrating the experimental…

This study is led by Dr. Shouchuang Wang (Sanya Nanfan Research Institute of Hainan University), revealing the role of epigenetic variation in tomato domestication and metabolic diversity from the perspective of population DNA methylation. The breeding history of tomato which is a world recognized model plant with high nutritional value…

As of 2019, the latest year for which data are available, more than 37 million people in the United States—or 11.3 percent of the country’s population—are living with diabetes, according to the U.S. Centers for Disease Control and Prevention. Among them, 8.5 million are adults who are undiagnosed or unaware…

An investigational outpatient endoscopic procedure may help eliminate the need for insulin in people with type 2 diabetes, early research suggests. Called re-cellularization via electroporation therapy (ReCET), the technology, manufactured by Endogenex, uses a specialized catheter to deliver alternating electric pulses to the duodenum to induce cellular regeneration. This process…

Ethics statement All animal experimentation was conducted according to the National Institutes of Health guidelines for the housing and care of laboratory animals. All experiments were performed in accordance with institutional regulations after review and approval by the Animal Studies Committee at Washington University School of Medicine in St Louis,…

Nanopore reads coupled to a novel computational method extends analyses of differential methylation to sparse CpGs (outside CpG islands) We analyzed tumor samples at diagnosis (T) and relapse (R) from three AML patients (UD5, UD10 and AML2) who received standard chemotherapy and relapsed with chemoresistant disease (supplementary Table 1). DNA from…

Allis, C. D. & Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 17, 487–500 (2016). Article  CAS  PubMed  Google Scholar  Zhao, Z. & Shilatifard, A. Epigenetic modifications of histones in cancer. Genome Biol. 20, 1–16 (2019). Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The…

Here is the tutorial (Analyzing WGBS data with bsseq) I want to use this method to visualize differential dmr regions on the same gene. Here is my code： if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“bsseq”) BiocManager::install(“bsseqData”) library(bsseq) library(bsseqData) data(BS.cancer.ex.fit) BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit) BS.cancer.ex.fit class(BS.cancer.ex.fit) ## data(BS.cancer.ex.fit) # BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit)…

Homer annotatePeaks for enrichment analysis 0 I want to test differentially methylated regions (DMRs; identified in whole genome bisulfite sequencing data) for enrichment of certain genomic features. For example, do I see more DMRs in promoters than I would expect by chance? It was suggested to me that a simple…

Both high FA and low FA intake increases de novo mutation rate and disrupt genome DNA methylation in the offspring. a Violin Plot of DNSNV/DNM (de novo mutation) counts among the three different FA dietary groups (sample size for each group was as follows; combined panel: 0.3 ppm group n = 26;…

DMRcaller Min. Reads per Cytosine 0 Hello! I’m a tech who’s starting a Ph.D. in August, so I am very new to bioinformatics. I’m wondering if anyone has some guidance on choosing min. reads per cytosine when calling DMRs. I am using DMRcaller on WGBS data. I have 3 biological…

Subset count data in DGEList using edgeR/DESeq2 1 @0f752196 Last seen 1 day ago United Kingdom Hello, I have an enormous methylation dataset (12.6Gb) that is proving too much for my computer to handle. This data is loaded in to R as a DGEList (with counts, samples, genes and a…

reVIeWS “Epigenetic Memory” Phenomenon in Induced Pluripotent Stem Cells E.A. Vaskova1,2,3, A.E. Stekleneva1,2,3, S.P. Medvedev1,2,3, S.M. Zakian1,2,3,* 1Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, prosp. Akad. Lavrentyeva, 10, Novosibirsk, Russia, 630090 2Meshalkin State Research Institute of Circulation Pathology, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 3Institute of…

Methylation is one of the most classical epigenetic modifications in eukaryotes. DNA methylation regulates gene expression and has important implications in both growth and disease-related research. DNA methylation affects the maturation of germ cells or embryonic cells subject to specific gene expression. It has also been widely studied and applied…

Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS  PubMed  PubMed Central  Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

DMRs, how common are they and how long? 1 Hi! Does anyone know how common differentially methylated regions (DMRs) (or just methylated regions) are? Say, in a 10,000bp region how many DMRs can one expect? Also, does anyone know about the distribution of the size/length of DMRs, i.e. how many…

The researchers of the‘UC Davis MIND during their research they used the genomic sequencing to find a DNA methylation signature in the placenta of infants diagnosed with autism. This hallmark has been linked to early fetal neurodevelopment. Thanks to this study, a new human gene linked to fetal brain development…

Methylation analysis pipelines The ENmix pipeline performs data preprocessing in a stepwise way, including ENmix background correction [1], RELIC dye bias correction [3], optional inter-array normalization, RCP probe-type bias correction [2], quality control, filtering of low-quality data points, and imputation. ENmix background correction employs a mixture of exponential and truncated…

Hi! I played around with the Illumina mouse demo data and ENmix. The following code worked for me and you should end up with normalized beta values for subsequent limma analysis (or DMR analysis folowing the ENmix vignette). #setwd() #download the Infinium_Mouse_Methylation_v1.0_A1_GS_Manifest_File.csv file from Illumina HP to working directory (=…

DOI: 10.18129/B9.bioc.ramr     Detection of Rare Aberrantly Methylated Regions in Array and NGS Data Bioconductor version: Release (3.13) ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions…

Using MethylKit with gemBS output files 0 Hi, I was just wondering if anyone is familiar with using gemBS output files for MethylKit such as the ones below *_3_lane_gembs_cpg.bed.gz *_3_lane_gembs_cpg.txt.gz With the following columns Contig Pos0 Pos1 Ref Call Flags Meth non_conv conv support_call total I tried running methylKit but…

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

Introduction In recent years, the morbidity and mortality of colon cancer have increased rapidly, both being ranked fourth worldwide. Although surgery-based comprehensive treatments improve the prognosis of colon cancer, because of the lack of available means for early diagnosis, the mortality level remains high for patients with advanced-stage cancer. The…