ArticleBMC bioinformatics2018
Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Methylation Mesa define functional regulatory elements for targeted gene activation.Nature communications · 2026Article
- Uncovering alterations in cancer epigenetics via trans-dimensional Markov chain Monte Carlo and hidden Markov models.Journal of the Royal Statistical Society. Series C, Applied statistics · 2026Article
- diffMONT: predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application.Bioinformatics (Oxford, England) · 2026Article
- Lack of caspase 8 directs neuronal progenitor-like reprogramming and small cell lung cancer progression.Nature communications · 2025Article
- MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets.Nucleic acids research · 2024Article
- Article
- Grafting based DNA methylation alteration of snoRNAs in upland cotton (Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation.BMC biology · 2024Article
- Base editor scanning charts the DNMT3A activity landscape.Nature chemical biology · 2023Article
- Epigenetic control of ataxin-1 in multiple sclerosis.Annals of clinical and translational neurology · 2022Article
- Integrative multi-omic analysis reveals neurodevelopmental gene dysregulation in CIC-knockout and IDH1-mutant cells.The Journal of pathology · 2022Article
- Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies.Small methods · 2022Review
- Identification of Novel Regulatory Regions Induced by Intrauterine Growth Restriction in Rat Islets.Endocrinology · 2022Article
- Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands.Nature genetics · 2021Article
- Changes in Phenotypes and DNA Methylation of In Vitro Aging Sperm in Common CarpInternational journal of molecular sciences · 2021Article
- Article
- Investigating Different DNA Methylation Patterns at the Resolution of Methylation Haplotypes.Frontiers in genetics · 2021Article
- Genome-Wide DNA Methylation Changes of Perirenal Adipose Tissue in Rabbits Fed a High-Fat Diet.Animals : an open access journal from MDPI · 2020Article
- Exposure to Gestational Diabetes Enriches Immune-Related Pathways in the Transcriptome and Methylome of Human Amniocytes.The Journal of clinical endocrinology and metabolism · 2020Article
- In utero Bisphenol A Exposure Is Linked with Sex Specific Changes in the Transcriptome and Methylome of Human Amniocytes.The Journal of clinical endocrinology and metabolism · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
backgroundIdentification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion.
resultsWe developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data.
conclusionsDefiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.