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genome-wide dna methylation patterns analysis  (Epigenomics ag)

 
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    Epigenomics ag genome-wide dna methylation patterns analysis
    Multi-omics researches on patients with Crohn's disease.
    Genome Wide Dna Methylation Patterns Analysis, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/methylation+patterns+analysis/genome+wide+dna+methylation+assays/pmc10238466-50-18-7
    Average 90 stars, based on 1 article reviews
    genome-wide dna methylation patterns analysis - by Bioz Stars, 2026-10
    90/100 stars

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    1) Product Images from "Multi-omics in Crohn's disease: New insights from inside"

    Article Title: Multi-omics in Crohn's disease: New insights from inside

    Journal: Computational and Structural Biotechnology Journal

    doi: 10.1016/j.csbj.2023.05.010

    Multi-omics researches on patients with Crohn's disease.
    Figure Legend Snippet: Multi-omics researches on patients with Crohn's disease.

    Techniques Used: Biomarker Discovery, Reversed-phase Chromatography, Activity Assay, Fractionation, Sequencing, RNA Sequencing, Multiplex Assay, Liquid Chromatography with Mass Spectroscopy, GWAS, Expressing, DNA Methylation Assay, Genome Wide, Functional Assay, Bacteria, Hydrophilic Interaction Liquid Chromatography, Shotgun Sequencing, Starch, Modification, Gas Chromatography-Mass Spectrometry, Clinical Proteomics, Control, Methylation, Derivative Assay, Gene Expression, Isolation

    Brief summary of the most common pipelines in omics.
    Figure Legend Snippet: Brief summary of the most common pipelines in omics.

    Techniques Used: Genome Wide, GWAS, Methylation, Sequencing, Selection, Polymerase Chain Reaction, Nuclear Magnetic Resonance, Gas Chromatography-Mass Spectrometry, Sample Prep, Extraction, Chromatography, Liquid Chromatography with Mass Spectroscopy, Data-independent acquisition, Mass Spectrometry, Quantitative Proteomics

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    other:

    Article Title: Genome-wide methylation profiling of HCV pathogenesis to develop diabetes and diabetic complications.
    Article Snippet: HCV is key pathological factor for inducting insulin resistance.. Such HCV induced insulin resistance is linked with metabolic syndrome, type2 diabetes mellitus, extrahepatic manifestations, hepatic fibrosis progression and development of hepatocellular carcinoma.. DNA methylation alterations can cause developmental abnormalities, tumors and other diseases.

    Article Title: Multi-omics in Crohn's disease: New insights from inside
    Article Snippet: , Epigenomics , Biopsies from 72 paired CD. Matching host transcriptome data from 71 samples , Genome-wide DNA methylation analysis.

    Article Title: Multi-omics in Crohn's disease: New insights from inside
    Article Snippet: Howell, Kate Joanne et al. 2018 , Epigenomics , 7 healthy children and 5 pediatric CD patients , Genome-wide DNA methylation patterns analysis , , • CD-associated DMPs showed a clear trend to be differentially methylated in CD-derived compared with control organoids. • CD- and UC-associated DMPs showed remarkable stability over time. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • DMRs, DEGs, and rDMRs in both colonic and ileal IECs for IBD risk loci enriched. • Variation by gut segment and reduction in species diversity for CD patients were revealed. • IECs underwent changes during IBD development and could be involved in pathogenesis..

    Article Title: Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis.
    Article Snippet: Air pollution might affect atherosclerosis through DNA methylation changes in cells crucial to atherosclerosis, such as monocytes.. We conducted an epigenome-wide study of DNA methylation in CD14+ monocytes and long-term ambient air pollution exposure in adults participating in the Multi-Ethnic Study of Atherosclerosis (MESA).. We also assessed the association between differentially methylated signals and cis-gene expression.

    Article Title: Advancing Thoracic Surgical Oncology in the Era of Precision Medicine
    Article Snippet: Epigenomics , Examines DNA methylation, histone modifications influencing gene expression. , Stratifies tumors by aggressiveness, potential for metastasis, and long-term recurrence risk, refining surgical planning. , Hypermethylation of tumor suppressor genes associated with poor outcomes and need for more aggressive surgical intervention..

    Article Title: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.
    Article Snippet: “Performance Comparisons of Methylation and Structural Variants from Low-Input Whole-Genome Methylation Sequencing.” Epigenomics 15 (1): 11–19. https://doi.org/10.2217/epi-2022-0453.

    Genome Wide:

    Article Title: Implementation of multi-omics in diagnosis of pediatric rare diseases.
    Article Snippet: .. Epigenomics explores genome-wide DNA modifications, transcriptomics analyzes RNA expression across all RNAs, proteomics uncovers protein structures, functions, interactions, and levels on a large scale, and metabolomics examines identification and quantification of metabolites in biological specimens. ..

    RNA Expression:

    Article Title: Implementation of multi-omics in diagnosis of pediatric rare diseases.
    Article Snippet: .. Epigenomics explores genome-wide DNA modifications, transcriptomics analyzes RNA expression across all RNAs, proteomics uncovers protein structures, functions, interactions, and levels on a large scale, and metabolomics examines identification and quantification of metabolites in biological specimens. ..

    Methylation:

    Article Title: Meeting abstracts of the clinical epigenetics international conference 2024
    Article Snippet: .. A20 Whole genome methylation profiling to enhance diagnostic yield in neurodevelopmental disorders Andreas Risch1, Marion Auburger1, Stephanie Kleinle1, Maximilian Witzel1, Bekim Sadikovic2, Ariane Hallermayr1, Teresa Neuhann1, Angela Abicht1,3 1MGZ—Medical Genetics Center, München, Germany; 2Clinical Genomics and Epigenomics, London Health Sciences Centre, Canada; 3Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-Universität, München, Germany Keywords: Episignature, Neurodevelopmental, Disorder, Methylation, Profiling Topic/s: Epigenetics of disease Epigenetic analysis in clinical diagnostics offers novel insights into complex genetic disorders, particularly neurodevelopmental delay (NDD) with or without congenital anomalies. ..

    Diagnostic Assay:

    Article Title: Meeting abstracts of the clinical epigenetics international conference 2024
    Article Snippet: .. A20 Whole genome methylation profiling to enhance diagnostic yield in neurodevelopmental disorders Andreas Risch1, Marion Auburger1, Stephanie Kleinle1, Maximilian Witzel1, Bekim Sadikovic2, Ariane Hallermayr1, Teresa Neuhann1, Angela Abicht1,3 1MGZ—Medical Genetics Center, München, Germany; 2Clinical Genomics and Epigenomics, London Health Sciences Centre, Canada; 3Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-Universität, München, Germany Keywords: Episignature, Neurodevelopmental, Disorder, Methylation, Profiling Topic/s: Epigenetics of disease Epigenetic analysis in clinical diagnostics offers novel insights into complex genetic disorders, particularly neurodevelopmental delay (NDD) with or without congenital anomalies. ..



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    Multi-omics researches on patients with Crohn's disease.

    Journal: Computational and Structural Biotechnology Journal

    Article Title: Multi-omics in Crohn's disease: New insights from inside

    doi: 10.1016/j.csbj.2023.05.010

    Figure Lengend Snippet: Multi-omics researches on patients with Crohn's disease.

    Article Snippet: Howell, Kate Joanne et al. 2018 , Epigenomics , 7 healthy children and 5 pediatric CD patients , Genome-wide DNA methylation patterns analysis , , • CD-associated DMPs showed a clear trend to be differentially methylated in CD-derived compared with control organoids. • CD- and UC-associated DMPs showed remarkable stability over time. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • DMRs, DEGs, and rDMRs in both colonic and ileal IECs for IBD risk loci enriched. • Variation by gut segment and reduction in species diversity for CD patients were revealed. • IECs underwent changes during IBD development and could be involved in pathogenesis..

    Techniques: Biomarker Discovery, Reversed-phase Chromatography, Activity Assay, Fractionation, Sequencing, RNA Sequencing, Multiplex Assay, Liquid Chromatography with Mass Spectroscopy, GWAS, Expressing, DNA Methylation Assay, Genome Wide, Functional Assay, Bacteria, Hydrophilic Interaction Liquid Chromatography, Shotgun Sequencing, Starch, Modification, Gas Chromatography-Mass Spectrometry, Clinical Proteomics, Control, Methylation, Derivative Assay, Gene Expression, Isolation

    Brief summary of the most common pipelines in omics.

    Journal: Computational and Structural Biotechnology Journal

    Article Title: Multi-omics in Crohn's disease: New insights from inside

    doi: 10.1016/j.csbj.2023.05.010

    Figure Lengend Snippet: Brief summary of the most common pipelines in omics.

    Article Snippet: Howell, Kate Joanne et al. 2018 , Epigenomics , 7 healthy children and 5 pediatric CD patients , Genome-wide DNA methylation patterns analysis , , • CD-associated DMPs showed a clear trend to be differentially methylated in CD-derived compared with control organoids. • CD- and UC-associated DMPs showed remarkable stability over time. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • MDS plots showed:(1) samples derived from controls clustered closely in each gut segment;(2) distinct clustering of samples by gut segment separating all TI-derived epithelium from colonic (i.e., AC and SC) samples; a subset of IBD samples distinctly separated from controls. • Analysis of ileal IECs revealed:(1) CD-specific changes in DNAm;(2) amongst identified rDMRs, several have previously been reported to be associated with IBD (e.g., CASP133 and APOA19). • Analysis of SC IECs revealed a major overlap between UC and CD signatures with only a single significant DEG (RARRES3). • DMRs, DEGs, and rDMRs in both colonic and ileal IECs for IBD risk loci enriched. • Variation by gut segment and reduction in species diversity for CD patients were revealed. • IECs underwent changes during IBD development and could be involved in pathogenesis..

    Techniques: Genome Wide, GWAS, Methylation, Sequencing, Selection, Polymerase Chain Reaction, Nuclear Magnetic Resonance, Gas Chromatography-Mass Spectrometry, Sample Prep, Extraction, Chromatography, Liquid Chromatography with Mass Spectroscopy, Data-independent acquisition, Mass Spectrometry, Quantitative Proteomics

    Comparison of orbital fibroblast global DNA methylation profiles with FDR <0.05. (A) DNA methylation in active GO orbital fibroblasts (n = 4), inactive GO orbital fibroblasts (n = 4) and healthy control orbital fibroblasts (n = 4) were compared. Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Genes with differential DNA methylation were further corrected for multiple testing using FDR < 0.05. (B) Methylation level of SLC39A8 . Methylation level ranges from 0 (unmethylated) to 1 (fully methylated). Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median. (C) SLC39A8 expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median.

    Journal: Frontiers in Endocrinology

    Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

    doi: 10.3389/fendo.2020.619989

    Figure Lengend Snippet: Comparison of orbital fibroblast global DNA methylation profiles with FDR <0.05. (A) DNA methylation in active GO orbital fibroblasts (n = 4), inactive GO orbital fibroblasts (n = 4) and healthy control orbital fibroblasts (n = 4) were compared. Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Genes with differential DNA methylation were further corrected for multiple testing using FDR < 0.05. (B) Methylation level of SLC39A8 . Methylation level ranges from 0 (unmethylated) to 1 (fully methylated). Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median. (C) SLC39A8 expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median.

    Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

    Techniques: Comparison, DNA Methylation Assay, Control, Methylation, Expressing, MANN-WHITNEY

    Hypermethylated genes in orbital fibroblasts from active GO in comparison to orbital fibroblasts from inactive GO and healthy controls with a fold difference ≥ 2. DNA methylation in active GO orbital fibroblasts (n = 4) was compared with inactive GO orbital fibroblasts (n = 4). Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Hypermethylated genes with differences in DNA methylation level of at least 2-fold in active GO orbital fibroblasts were clustered as shown in the heatmap.

    Journal: Frontiers in Endocrinology

    Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

    doi: 10.3389/fendo.2020.619989

    Figure Lengend Snippet: Hypermethylated genes in orbital fibroblasts from active GO in comparison to orbital fibroblasts from inactive GO and healthy controls with a fold difference ≥ 2. DNA methylation in active GO orbital fibroblasts (n = 4) was compared with inactive GO orbital fibroblasts (n = 4). Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Hypermethylated genes with differences in DNA methylation level of at least 2-fold in active GO orbital fibroblasts were clustered as shown in the heatmap.

    Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

    Techniques: Comparison, DNA Methylation Assay, Methylation

    Hypomethylated genes in orbital fibroblasts from active GO in comparison to orbital fibroblasts from inactive GO and healthy controls with a fold difference ≥ 2. DNA methylation in active GO orbital fibroblasts (n = 4) were compared with inactive GO orbital fibroblasts (n = 4). Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Hypomethylated genes with differences in DNA methylation level of at least 2-fold in active GO orbital fibroblasts were clustered as shown in the heatmap.

    Journal: Frontiers in Endocrinology

    Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

    doi: 10.3389/fendo.2020.619989

    Figure Lengend Snippet: Hypomethylated genes in orbital fibroblasts from active GO in comparison to orbital fibroblasts from inactive GO and healthy controls with a fold difference ≥ 2. DNA methylation in active GO orbital fibroblasts (n = 4) were compared with inactive GO orbital fibroblasts (n = 4). Global DNA methylation was measured using the Illumina Infinium Human Methylation 450K beadchip on bisulphite-treated DNA and analyzed by GenomeStudio methylation analysis package. Hypomethylated genes with differences in DNA methylation level of at least 2-fold in active GO orbital fibroblasts were clustered as shown in the heatmap.

    Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

    Techniques: Comparison, DNA Methylation Assay, Methylation

    Comparison of DNA methylation, mRNA expression and proteomic data. (A) Comparison of hypermethylated genes, mRNA expression and proteomic data. Gene expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median. (B) Comparison of hypomethylated genes, mRNA expression and proteomic data. Gene expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median.

    Journal: Frontiers in Endocrinology

    Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

    doi: 10.3389/fendo.2020.619989

    Figure Lengend Snippet: Comparison of DNA methylation, mRNA expression and proteomic data. (A) Comparison of hypermethylated genes, mRNA expression and proteomic data. Gene expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median. (B) Comparison of hypomethylated genes, mRNA expression and proteomic data. Gene expression was determined by real-time quantitative (RQ)-PCR and normalized to the control gene ABL . Data from mRNA expression was analyzed using ANOVA and subsequently analyzed with the Mann Whitney U test. Individual symbols represent orbital fibroblast cultures from individual patients. Horizontal bar depicts the median.

    Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

    Techniques: Comparison, DNA Methylation Assay, Expressing, Gene Expression, Control, MANN-WHITNEY

    Methylation based network analysis. (A) Network 1 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to neurological disease, organismal injury and abnormalities, and nervous system development and function Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (B) Network 2 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to embryogenic development, nervous system development and function, and organ development. Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (C) Network 3 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to cardiovascular system development and function, organismal development, and cellular assembly and organization. Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (D) Network 4 derived from hypomethylated genes in orbital fibroblasts from active GO: linked to cellular growth and proliferation, nervous system development and function, and cell-to-cell signaling and interaction. Network analysis was further performed on these differentially hypomethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information.

    Journal: Frontiers in Endocrinology

    Article Title: Integrative Analysis of Proteomics and DNA Methylation in Orbital Fibroblasts From Graves’ Ophthalmopathy

    doi: 10.3389/fendo.2020.619989

    Figure Lengend Snippet: Methylation based network analysis. (A) Network 1 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to neurological disease, organismal injury and abnormalities, and nervous system development and function Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (B) Network 2 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to embryogenic development, nervous system development and function, and organ development. Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (C) Network 3 derived from hypermethylated genes in orbital fibroblasts from active GO: linked to cardiovascular system development and function, organismal development, and cellular assembly and organization. Network analysis was further performed on these differentially hypermethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information. (D) Network 4 derived from hypomethylated genes in orbital fibroblasts from active GO: linked to cellular growth and proliferation, nervous system development and function, and cell-to-cell signaling and interaction. Network analysis was further performed on these differentially hypomethylated genes (highlighted in grey) using Ingenuity (Qiagen) filtering only for those networks and pathways that are based on experimentally obtained information.

    Article Snippet: Furthermore, bisulphite-treated DNA was analyzed for methylation pattern with the Illumina Infinium Human Methylation 450K beadchip.

    Techniques: Methylation, Derivative Assay