Identify differentially methylated regions. Medical search. Frequent questions

Therefore, a more biologically appropriate approach is to determine differentially methylated regions (DMRs) of multiple CpG sites. (biomedcentral.com)
Although several statistical approaches exist to identify DMRs between two sample groups, many of these have substantial limitations. (biomedcentral.com)
However, due to the extensive epigenetic reprogramming that occurs during embryogenesis, we hypothesized that the different methylation regions (DMRs) identified in the blastocysts may not maintain in adulthood. (animal-reproduction.org)
Here, we aimed to characterize DMRs previously identified in embryos, in the blood and sperm of adult progenies of two groups of heifers (low S/Co and control). (animal-reproduction.org)
[ 2 ] They also noted that the mole was biparental, and there was a specific maternal loss of DNA methylation of differentially methylated regions (DMRs). (medscape.com)
We identified 14 significantly differentially methylated regions (DMRs) within genes associated with cumulative blast exposure in participants with high relative to low cumulative blast exposure. (frontiersin.org)
In comparing lifetime blast exposure at baseline (prior to exposure in current training), and top associated symptoms, we identified significant DMRs associated with tinnitus, sleep difficulties, and headache. (frontiersin.org)
Gene expression profiling (RNA-seq) and genome-wide sequencing of methylated DNA (MBD-seq) identified dynamic changes in the cardiac methylome during postnatal development [2545 differentially methylated regions (DMRs) from P1 to P14 in the mouse]. (nih.gov)
The vast majority (~80%) of DMRs were hypermethylated between P1 and P14, and these hypermethylated regions were associated with transcriptional shut down of important developmental signaling pathways, including Hedgehog, bone morphogenetic protein, TGF-β, fibroblast growth factor, and Wnt/β-catenin signaling. (nih.gov)
Moreover, pair-wise comparison of controls and HD iPS allowed to identify a panel of differentially methylated regions (DMRs) during the different phases of neuronal commitment. (bmj.com)
Using Methylated DNA Capture sequencing (MethylCap-seq) we discovered a diverse landscape of DNA methylation across the tadpole neural cell genome, and pairwise stage comparisons identified several thousand differentially methylated regions (DMRs). (nih.gov)
Using RNA sequencing, we found negative correlations between differentially expressed genes and DMRs localized to gene bodies and regions upstream of transcription start sites. (nih.gov)
We identified differentially methylated regions (DMRs) and differentially hydroxymethylated regions (DHMRs) between ILC and NK cell subsets and correlated them with transcriptional signatures. (stanford.edu)
Probes common across EWAS were meta-analyzed using METAL, and differentially methylated and variable regions (DMRs and DVRs, respectively) were identified using comb-p. (columbia.edu)
Using meta-analyzed results, we identified 11 DMRs and 11 DVRs in PBMC samples, and 16 DMRs and 19 DVRs in PBMC and buccal cell samples. (columbia.edu)
Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. (weigelworld.org)
We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. (weigelworld.org)
We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype-epigenotype associations. (weigelworld.org)
The promoter region of MEG3 is rich in CpG islands, and the specific methylated and unmethylated CpG islands of differentially methylated regions (DMRs) are located upstream of the MEG3 gene (IG-DMR and MEG3-DMR) ( 17 , 18 ). (spandidos-publications.com)
Subsequently, the researchers identified differentially methylated regions (DMRs) between the long and short survivor groups and assessed the biological pathways and functions enriched in those regions. (docwirenews.com)
We are investigating the whole genome DNA methylation changes in infertile individuals in comparison with fertile controls in order to identify the differentially methylated regions (DMRs) that correlate with human male infertility. (cdri.res.in)

These 'CpG islands' are largely unmethylated in somatic cells, but those near genes under long-term transcriptional repression are frequently methylated. (biomedcentral.com)
Capra E, Lazzari B, Turri F, Cremonesi P, Portela AMR, Ajmone-Marsan P, Stella A, Pizzi F. Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus. (animal-reproduction.org)
In this study, three independent microarray studies of CD were integrated and 9912 differentially expressed genes (DEGs) were analysed by NetworkAnalyst to screen candidate crucial genes. (hindawi.com)
We identified ELAVL1 and APP, previously implicated in regulating the activation of innate immunity [ 13 , 14 ] and T cells [ 15 ], the most significant up- and downregulated genes. (hindawi.com)
Functional characterization of the identified regions found relationships between methylation at these loci and nearby genetic variation contributing to chronic painful TMD and with gene expression of proximal genes. (iasp-pain.org)
Additionally, we found that differentially methylated regions associated with the genes CCDC68 and COMT track with sleep difficulties, and those within FMOD and TNXB track with pain and headache. (frontiersin.org)
In the sperm of rats injected with THC and those nicotine-exposed, significant differential methylation at five of seven neurodevelopmentally active genes that were initially identified as significantly altered by oral gavage was identified. (duke.edu)
Enrichment of both autism candidate genes and genes possessing bivalent chromatin was identified in the human RRBS dataset of genes significantly differentially methylated in sperm of cannabis users. (duke.edu)
We found that the most significant differentially methylated sites had a remarkable enrichment in type I interferon (IFN) pathway genes. (frontiersin.org)
We also identified a number of variants in the coding region of genes which could have effects on translation of genes. (biomedcentral.com)
We then used the identified variants to construct a strain-specific CD-1 reference genome, and associated annotation files, including genes and the full set of identified CD-1 variants. (biomedcentral.com)
The imprinted region on chromosome 14q32 and expression of imprinted genes on the maternal allele (upper) and paternal allele (lower) for six genes. (bmj.com)
One approach is to evaluate the DNA methylation of cytosine-guanine dinucleotides (CpGs) in the promoter, exons, introns, enhancers and CpG island shore regions of genes as they can have a significant impact on the regulation of gene expression. (biomedcentral.com)
In this study, we performed quantitative methylation analyses of six differentially methylated imprinted genes (H19, MEG3, LIT1, NESP55, PEG3 and SNRPN), one hypermethylated pluripotency gene (OCT4) and one hypomethylated tumor suppressor gene (APC) in chorionic villus, fetal and adult cortex, and adult blood samples. (uni-wuerzburg.de)
Furthermore, reactive eosinophilia samples could be differentiated from known- and suspected clonal eosinophilia samples based on 285 differentially methylated CpG sites corresponding to 128 differentially methylated genes. (oncotarget.com)
Using Ingenuity pathway analysis, we found that differentially methylated genes were highly enriched in functional pathways such as cancer, cell death and survival, and hematological disease. (oncotarget.com)
Interestingly, many of the identified genes are associated with cancer risk and/or interact with estrogen. (epigenie.com)
The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes (mainly in the promoter and body regions, respectively) with negative and positive correlation, respectively. (unesp.br)
A similar integrative analysis uncovered 40 of 254 differentially expressed genes, which are potentially regulated by DNA methylation in BRAFV600E-positive tumors. (unesp.br)
Additionally, we found that 68.2% of intragenic sequences exhibiting tissue-specific DNA methylation identified from a genome-wide screen harbored features of promoters more commonly associated with the 5'-end of genes. (escholarship.org)

After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. (biomedcentral.com)
To date, the agnostic search of the genome by genome-wide association (GWA) to identify common variants associated with LDD has not been fruitful. (bmj.com)
Whole-genome methylation profiling reveals regions associated with painful temporomandibular disorders and active recovery processes. (iasp-pain.org)
Reduced-Representation Methylation Sequencing (RRMS) with Oxford Nanopore enables cost-effective, genome-wide characterisation of methylation patterns across regions of interest. (nanoporetech.com)
Analysis of both human and mouse whole genome bisulfite sequencing datasets reveals read-level signatures, which are mostly orthogonal to classical differentially methylated regions, are enriched at cell type-specific enhancers and allow estimation of proportional cell composition in synthetic mixtures and improved prediction of gene expression. (usda.gov)
Whole-genome profiling of DNA methylation and hydroxymethylation identifies distinct regulatory programs among innate lymphocytes. (stanford.edu)
We performed deep genomic DNA sequencing of CD-1 mice and used the data to identify genome-wide SNPs, indels, and germline transposable elements relative to the mm10 reference genome. (biomedcentral.com)
We used the identified variants to construct a CD-1-specific reference genome, which can improve accuracy and reduce bias when aligning genomics data derived from CD-1 mice. (biomedcentral.com)
However, the prior study only examined single nucleotide polymorphisms (SNPs) previously identified in other mouse strains, and to date, a full, genome-wide identification of genetic variants that exist between CD-1 mice has not been done. (biomedcentral.com)
We validated the CD-1 reference genome and the identified variants by comparative mapping of a wide range of CD-1 genomics datasets between the CD-1 and standard mm10 reference genomes. (biomedcentral.com)
Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. (biorxiv.org)
Whole-exome sequencing and genome-wide methylation analyses identify novel disease associated mutations and methylation patterns in idiopathic. (oncotarget.com)
Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between the Eyach15-2 accession and the reference accession Col-0. (weigelworld.org)
Results: The comparisons between PTC and NT revealed 4995 methylated probes (88% hypomethylated in PTC) and 1446 differentially expressed transcripts cross-validated by the The Cancer Genome Atlas data. (unesp.br)
One of our recent studies has identified a number of such loci across human genome (unpublished data). (cdri.res.in)
Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. (who.int)

Although CpG sites occur less frequently than expected in mammalian genomes, more than half of gene promoters contain short, clustered regions with high concentrations of these sites [ 1 ]. (biomedcentral.com)
NetworkAnalyst identified ELAV-like RNA binding protein 1 (ELAVL1) as the most crucial upregulated gene and amyloid- β precursor protein (APP) as the most crucial downregulated gene in peripheral blood of CD patients. (hindawi.com)
We identified a variant in the PARK2 gene (p=2.8×10 −8 ) associated with LDD. (bmj.com)
One gene identified as being significantly differentially methylated was an autism candidate gene, Discs-Large Associated Protein 2 (DLGAP2). (duke.edu)
Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. (biorxiv.org)
We found that surgical NEC has a considerable impact on the epigenome by broadly increasing DNA methylation levels, although these effects are less pronounced in genomic regions associated with the regulation of gene expression. (biomedcentral.com)
We also identified numerous transcriptional changes in NEC and clear associations between gene expression and DNA methylation. (biomedcentral.com)
Sperm samples not leading to a pregnancy, in particular in the OAT group, had significantly more epimutations in the paternally methylated GTL2 gene than samples leading to a live birth. (uni-wuerzburg.de)
In addition to the promoter region, gene body and 3'UTR methylation have also the potential to influence the gene expression levels (both, repressing and inducing). (unesp.br)
As DNA methylation is an important regulatory mechanism for gene expression, the identified DNA methylation alterations might contribute to functional changes in the human brain and thereby to the associated behavioral aspects of addiction," first author Eric Poisel, a PhD student at the Central Institute of Mental Health in Mannheim, said in the release. (medscape.com)

Imprinted expression is controlled by a primary imprinting control region (ICR) (intergenic differentially methylated region or IG-DMR) located between DLK1 and GTL2/MEG3 , which is normally methylated only on the paternal allele. (bmj.com)
Furthermore, the results of methylation‑specific PCR revealed that the abnormal methylation status of the MEG3 promoter region was present in eight of the 39 bone marrow samples collected. (spandidos-publications.com)
lncRNA MEG3 has been identified as a tumor suppressor in various types of cancer, including meningioma ( 12 ), breast cancer ( 13 ), bladder cancer ( 14 ) and hepatocellular carcinoma ( 15 ). (spandidos-publications.com)

Following alignment, DMRfinder extracts methylation counts and performs a modified single-linkage clustering of methylation sites into genomic regions. (biomedcentral.com)
Contrasting two replicates of the same sample yielded minimal genomic regions with DMRfinder, whereas two alternative software packages reported a substantial number of false positives. (biomedcentral.com)
We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. (biorxiv.org)
Seventeen (85%) of these genomic regions were hypermethylated and three (15%) were hypomethylated. (medscape.com)

Long-range epigenetic changes, structural variants, and single nucleotide polymorphisms can be identified and phased in a single dataset. (nanoporetech.com)
We conducted an integrative analysis of the multiple-autoimmune disease methylation dataset including GD, RA, SLE, and SSc samples, to identify the common methylation patterns of autoimmune diseases. (frontiersin.org)

In a recent study, we identified that about two thousand transcripts are differentially expressed between fertile and infertile sperm. (cdri.res.in)
A number of transcripts that participate in a host of cellular processes including reproduction and development were differentially expressed between fertile and infertile individuals. (cdri.res.in)

For example, network analyses identified HNF4A and PTBP1 as effective biomarkers for Parkinson's disease [ 11 ] and 873 DEGs genetically related to insulin resistance [ 12 ]. (hindawi.com)

Among the computational approaches for identifying differentially methylated regions from high-throughput bisulfite sequencing datasets, DMRfinder is the first that integrates all the post-alignment steps in a single package. (biomedcentral.com)
Quantitative bisulfite pyrosequencing confirmed that an intronic region of DLGAP2 was significantly hypomethylated in the sperm of cannabis exposed men compared to controls. (duke.edu)
Bisulfite pyrosequencing identified significant changes in rat sperm DNA methylation at Dlgap2, as well as significant losses of methylation at the same locus in F1 nucleus accumbens (NAc) tissues. (duke.edu)
Bisulfite pyrosequencing of sperm DNA from rats exposed to injected THC or vehicle control was performed to examine methylation at regions identified by RRBS. (duke.edu)

Maternal uniparental disomy of chromosome 14, paternal deletions and loss of methylation at the intergenic differentially methylated region (IG-DMR) result in a human phenotype of low birth weight, hypotonia, early puberty and markedly short adult stature. (bmj.com)

Sperm DNA from rats exposed to nicotine or vehicle control underwent pyrosequencing at the same regions. (duke.edu)

In addition, CD8 + T cell transcriptional signatures were identified as reliable prognostic biomarkers in the blood of CD patients [ 6 , 7 ]. (hindawi.com)

A majority of loci were similarly differentially methylated in acute TMD consistent with observed transience or persistence of symptoms at follow-up. (iasp-pain.org)
In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease. (biorxiv.org)

We associated lineage-determining transcription factors (LDTFs) with demethylation and demonstrated unique patterns of DNA methylation/hydroxymethylation in relationship to open chromatin regions (OCRs), histone modifications and TF-binding sites. (stanford.edu)
Using Nanopore sequencing reads, DNA methylation was quantified at 1,779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. (biorxiv.org)
You will learn to use approaches for the identification of differentially methylated regions (dmrseq, MethylSig, DSS), more recent algorithms that analyse DNA methylation patterns at the level of individual sequencing reads (CluBCpG), as well as multiomic integration and network modelling strategies (MEGENA). (sfbi.fr)
Using patterns of DNA methylation as a measure of the biological age of cells, a total of 20 differentially methylated regions were significantly associated with CUD status after multiple testing correction. (medscape.com)

These intestinal samples will help to further identify the precise molecular signaling pathways involved in the pathogenesis of sNEC, with the hope to identify infants at the highest risk for the development of this devastating disease. (biomedcentral.com)
An integrative and cross-validation analysis were performed aiming to identify molecular drivers and pathways that are PTC-related. (unesp.br)

Similarly, we identified 9,295 differentially methylated sites between GD/SSc patients and controls in CD8+ T cells. (frontiersin.org)

Davis TL, Yang GJ, McCarrey JR, Bartolomei MS. The H19 methylation imprint is erased and re‐established differentially on the parental alleles during male germ cell development. (animal-reproduction.org)

Specifically, pan-mammalian epigenetic clocks determine the age of tissues from all mammalian species by analyzing cytosine methylation in DNA regions that are highly conserved New age estimation tools have been developed continuously, which also facilitate the prognosis of certain diseases. (wikipedia.org)
Using nanopore sequencing, researchers have directly identified DNA and RNA base modifications at single-nucleotide resolution, including 5mC, 5hmC, 6mA, and BrdU in DNA, and m6A in RNA, with detection of further natural or synthetic epigenetic modifications possible through training basecalling algorithms. (nanoporetech.com)
The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methylated regions). (usda.gov)
The identified epigenetic signature of Down syndrome includes differentially methylated regions that, although enriched on chromosome 21, interest most of the other chromosomes and can be functionally linked to the developmental and haematological defects characteristic of the disease. (nih.gov)
Although EWAS have consistently identified CpGs associated with arsenic exposure after adjusting for multiple comparisons, a common epigenetic signature of arsenic exposure has not emerged across different studies or regions. (biomedcentral.com)

Soil Virus Offers Insight into Maintaining Microorganisms Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health. (doe.gov)

Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. (bioconductor.org)
1.2.2 Identifying differential regions (e.g. (uni-freiburg.de)

Our approach suggests that standardizing analytical pipelines can aid in identifying biological meaningful signals. (columbia.edu)

The single-base resolution of the data allows for testing individual CpG sites, but regulated methylation targets are most commonly clustered into short regions. (biomedcentral.com)
We identified 15,289 differentially methylated sites between multiple-autoimmune disease patients and controls in CD4+ T cells. (frontiersin.org)

The majority of these probes was found in non-promoters regions, distant from CGI and enriched by enhancers. (unesp.br)

Conclusions: DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC, especially in tumors harboring BRAFV600E. (unesp.br)

In a recent study, we analyzed the AZFc region of the Y-chromosome for complete (b2/b4) and distinct partial deletions (gr/gr, b1/b3, b2/b3). (cdri.res.in)

Specifically, we identified DNA methylation differences in intestinal epithelial cell genomic DNA within resected ileum or colon that may provide new insights into the biology and mechanisms of NEC pathogenesis. (biomedcentral.com)
This notably includes a variety of strategies to identify changes in DNA methylation differences as a function of exposure to drugs of abuse. (sfbi.fr)
There were persistent differences in screening test use by metropolitan residence and census regions despite similar temporal trends. (cdc.gov)

Using a two-step process of (1) harmonized data processing and analysis and (2) meta-analysis, we leverage four DNAm datasets from two continents of individuals exposed to high levels of As prenatally and during adulthood to identify DMPs and DVPs associated with arsenic exposure. (columbia.edu)

Several distinct clinical phases of MM have been identified, including monoclonal gammopathy of undetermined significance and smoldering multiple myeloma ( 3 ). (spandidos-publications.com)
Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes. (who.int)

Probes in one region are optionally annotated to the same functional class(es). (bioconductor.org)

We have identified millions of previously unidentified CD-1 variants with the potential to confound studies involving CD-1. (biomedcentral.com)

The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. (bioconductor.org)

The analysis of the world literature of 51 cases identifies the key features that will enhance diagnosis and potentially improve treatment. (bmj.com)

To identify the mechanism that controls its distinctive T-lineage expression, we corrected the identified Bcl11b transcription start site and mapped a cell-type-specific differentially methylated region bracketing the Bcl11b promoter. (ca.gov)

In this thesis we identified an unexpected mechanism underlying the structural changes. (uantwerpen.be)

Exome sequencing and SNP panel based screening of mutations/polymorphisms has identified a number of significant genetic risk factors for male infertility (Gupta et al, 2013). (cdri.res.in)

BMI was additively associated with structure of many of the same brain regions as schizophrenia, but the cortical and subcortical alterations in schizophrenia were more widespread and pronounced. (escholarship.org)

Looping interactions between promoter-proximal elements including the differentially methylated region and downstream elements in the Major Peak are required to recapitulate the T-cell specific expression of Bcl11b in stable reporter assays. (ca.gov)

ASXL1 MT are associated with a loss of repressive histone methylation and increase in permissive histone methylation and acetylation in promoter regions. (nature.com)
We identified a 1.9-kb region 850 kb downstream of Bcl11b, 'Major Peak', distinguished by its dynamic histone marking pattern in development that mirrors the pattern at the Bcl11b promoter. (ca.gov)

Results Six miRNAs were differentially expressed between LR and HR. However, after adjustment for Tanner stage, the association was maintained only for miR-126-3p and miR-221-3p with a higher expression in HR group compared to LR group. (unav.edu)

Notably , NTSR1 and SPON1 were significantly differentially methylated in high relative to low blast exposed groups, suggesting that sleep dysregulation may be altered in response to chronic cumulative blast exposure. (frontiersin.org)

A third approach is to first smooth methylation levels prior to conducting t -tests, as implemented in the R/Bioconductor package bsseq [ 8 ], but this may lead to artifacts in regions of sparse data, especially with targeted MethylC-seq datasets. (biomedcentral.com)
Horvath spent over 4 years collecting publicly available Illumina DNA methylation data and identifying suitable statistical methods. (wikipedia.org)

DMRs21

Genes20

Genome16

Gene10

MEG33

Genomic regions4

Dataset2

Transcripts2

Analyses1

Bisulfite4

Intergenic1

Sperm1

Transcriptional1

Loci2

Patterns4

Pathways2

Similarly1

Alleles1

Epigenetic5

Researchers1

Differential2

Biological1

Sites2

Enhancers1

Conclusions1

Deletions1

Differences3

Associated with arsenic exposure1

Distinct2

Functional1

Variants1

Samples1

Analysis1

Cell type-specific1

Mechanism1

Significant1

Alterations1

Interactions1

Histone2

Results1

Notably1

Data2