Tag: CpG

Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease

This article was originally published here Brief Bioinform. 2022 Jan 17:bbab554. doi: 10.1093/bib/bbab554. Online ahead of print. ABSTRACT Health outcomes are frequently shaped by difficult to dissect inter-relationships between biological, behavioral, social and environmental factors. DNA methylation patterns reflect such multivariate intersections, providing a rich source of novel biomarkers and…

Continue Reading Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease

Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity

Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…

Continue Reading Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity

KINNEY_DNMT1_METHYLATION_TARGETS

Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…

Continue Reading KINNEY_DNMT1_METHYLATION_TARGETS

The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics

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…

Continue Reading The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics

Frontiers | The cGAS-STING Pathway: A Promising Immunotherapy Target

Introduction Invaded by exogenous or endogenous pathogens, the host immune system will be activated accordingly to resist harm and maintain homeostasis, which includes innate immunity and adaptive immunity. As the first line of host immune defense, innate immunity plays a critical role in recognizing extracellular and intracellular pathogens (1, 2)….

Continue Reading Frontiers | The cGAS-STING Pathway: A Promising Immunotherapy Target

PNAS Papers on Long Cell-Free DNA in Maternal Plasma, Genetic Propensity for Voting

The discovery of a large population of long, cell-free DNA (cfDNA) molecules in maternal plasma, along with a method to identify the molecules’ tissues of origin, is reported in this week Proceedings of the National Academy of Sciences. To date, studies of circulating cfDNA have focused on short molecules of…

Continue Reading PNAS Papers on Long Cell-Free DNA in Maternal Plasma, Genetic Propensity for Voting

Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark

Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark 0 Hello, previously, I was using Bismark with the ‘–comprehensive’ option to generate the individual bedgraph files from which we made the bigWigs. For one particular figure, my boss wants me to generate merged bdg files so that we…

Continue Reading Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark

Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

Continue Reading Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

Interpreting TFBS enrichment from random genomic regions

Hi all, To make a long story short, my lab has developed a computational method for analyzing WGBS data that results in genomic regions of interest. These are regions defined by sequencing reads with mixed methylation states (i.e. consecutive CpGs having non-matching methylation). My boss wants me to use some…

Continue Reading Interpreting TFBS enrichment from random genomic regions

Difference in Bismark output methylation call files and coverage files

Difference in Bismark output methylation call files and coverage files 1 Hi biostars! I am working with RRBS data and have used Bismark for methylation calls. I have compared the two output files with cytosines in a CpG-context and the coverage files (which only consider cytosines in a CpG context),…

Continue Reading Difference in Bismark output methylation call files and coverage files

mitochondrial dna damage triggers an ifn mediated immune response

2.6 Mitochondrial Damage-Induced Mitochondrial DNA Release is Central to Chronic Kidney Disease-Induced Type-I-Interferon Response in Vascular Smooth Muscle Cells DNA released from nuclear or mitochondria is the main source of endogenous DNA that activates cGAS-STING pathway. This is thought to be mediated by the presence 75 of leaked mitochondrial DNA…

Continue Reading mitochondrial dna damage triggers an ifn mediated immune response

RRBS data analysis using Bismark and methylkit

RRBS data analysis using Bismark and methylkit 0 Once we have read in the cytosine report files with methRead(), how to generate a table/dataframe of beta values or equivalent for all samples as columns and CpG sites as rows? Is the percMethylation() function the correct function to use? Beta values…

Continue Reading RRBS data analysis using Bismark and methylkit

Methylkit (differential methylation analysis) error in data frame

Methylkit (differential methylation analysis) error in data frame 0 Hi Friends, I am performing the differential methylation analysis using methylkit but it is throwing error in data frame. ” Error in [.data.frame(data, , 6) : undefined columns selected”. Can anyone help me to solve this error. Following is my R…

Continue Reading Methylkit (differential methylation analysis) error in data frame

Using MethylKit with gemBS output files

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…

Continue Reading Using MethylKit with gemBS output files

Resistance training rejuvenates the mitochondrial methylome in aged human skeletal muscle

doi: 10.1096/fj.202100873RR. Bradley A Ruple  1 , Joshua S Godwin  1 , Paulo H C Mesquita  1 , Shelby C Osburn  1 , Christopher G Vann  1 , Donald A Lamb  2 , Casey L Sexton  1 , Darren G Candow  3 , Scott C Forbes  4 , Andrew D Frugé  2 , Andreas N Kavazis  1 , Kaelin C Young …

Continue Reading Resistance training rejuvenates the mitochondrial methylome in aged human skeletal muscle

Integrated bioinformatics analysis to identify abnormal CC

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…

Continue Reading Integrated bioinformatics analysis to identify abnormal CC

Epigenome-wide association study of mitochondrial genome copy number

This article was originally published here Hum Mol Genet. 2021 Aug 20:ddab240. doi: 10.1093/hmg/ddab240. Online ahead of print. ABSTRACT We conducted cohort- and race-specific epigenome-wide association analyses of mtDNA copy number (mtDNA CN) measured in whole blood from participants of African and European origins in five cohorts (n = 6182,…

Continue Reading Epigenome-wide association study of mitochondrial genome copy number

New Mac program for molecular biologists

Tool:New Mac program for molecular biologists 12 I would like to present here a program – BioLabDonkey – for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac – Swift. The program can be downloaded from mac App Store – apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12…

Continue Reading New Mac program for molecular biologists

ProcessMethylation450Data function of TCGA-Assembler causing subscript out of bound error

ProcessMethylation450Data function of TCGA-Assembler causing subscript out of bound error 0 ProcessMethylation450Data function of TCGA-Assembler causing subscript out of bound error. However, if a take a little smaller subset of data, it is working fine. list_methylation_450 <- ProcessMethylation450Data(inputFilePath = “./QuickStartExample/Part1_DownloadedData/TCGABRCA.txt”, outputFileName = paste(sCancer, “methylation_450”, sep = “__”), outputFileFolder = sPath2)…

Continue Reading ProcessMethylation450Data function of TCGA-Assembler causing subscript out of bound error

bedGraphToBigWig Tutorial and Report

It is too easy to make error report in the bedGraphToBigWig process. I want to save the time for the fresh people. The following procedure would be work well for majority situations.  1, bedGraph should be without header before sorting awk ‘NR!=1’ input.bedGraph > input.deheader.bedGraph 2, bedGraph should be sorted sort…

Continue Reading bedGraphToBigWig Tutorial and Report