ArticleNucleic acids research2015
Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
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
56 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies.BMC research notes · 2021Pooled it
- Differential transcriptional and epigenetic signatures in CD4Journal of translational autoimmunity · 2026Article
- Multi-omics identifies promoter methylation and gene expression changes associated with human skeletal muscle atrophy.Experimental physiology · 2026Article
- Distinct Regulatory DNA Methylation Signatures Across Multiple Sclerosis, Neuromyelitis Optica, and Neurological Post-Acute Sequelae of COVID-19.Journal of clinical medicine · 2026Article
- DEVELOPMENT AND APPLICATION OF BRAIN TISSUE BASED MULTI-OMICS PROFILE SCORES FOR ALZHEIMER'S DISEASE.Research square · 2026Article
- Epigenetic signatures of maternal-fetal health: insights from cord blood and placenta.Epigenetics · 2025Article
- Conceptualizing Experimental Controls Using the Potential Outcomes Framework.The American statistician · 2025Article
- ComBat-met: adjusting batch effects in DNA methylation data.NAR genomics and bioinformatics · 2025Article
- Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles.Nature communications · 2025Article
- Potentially causal associations between placental DNA methylation and schizophrenia and other neuropsychiatric disorders.Nature communications · 2025Article
- Genome-Wide DNA Methylation Identifies Potential Disease-Specific Biomarkers and Pathophysiologic Mechanisms in Irritable Bowel Syndrome, Inflammatory Bowel Disease, and Celiac Disease.Neurogastroenterology and motility · 2025Article
- Article
- Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles.Research square · 2024Article
- Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling.BMC genomics · 2024Article
- Cancer predisposition signaling in Beckwith-Wiedemann Syndrome drives Wilms tumor development.British journal of cancer · 2024Article
- DNA methylation modulated genetic variant effect on gene transcriptional regulation.Genome biology · 2023Article
- Epigenomic variability is associated with age-specific naïve CD4 T cell response to activation in infants and adolescents.Immunology and cell biology · 2023Article
- Potentially causal associations between placental DNA methylation and schizophrenia and other neuropsychiatric disorders.medRxiv : the preprint server for health sciences · 2023Article
- AC-PCoA: Adjustment for confounding factors using principal coordinate analysis.PLoS computational biology · 2022Article
- Longitudinal analysis of blood DNA methylation identifies mechanisms of response to tumor necrosis factor inhibitor therapy in rheumatoid arthritis.EBioMedicine · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Due to their relatively low-cost per sample and broad, gene-centric coverage of CpGs across the human genome, Illumina's 450k arrays are widely used in large scale differential methylation studies. However, by their very nature, large studies are particularly susceptible to the effects of unwanted variation. The effects of unwanted variation have been extensively documented in gene expression array studies and numerous methods have been developed to mitigate these effects. However, there has been much less research focused on the appropriate methodology to use for accounting for unwanted variation in methylation array studies. Here we present a novel 2-stage approach using RUV-inverse in a differential methylation analysis of 450k data and show that it outperforms existing methods.
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.