ArticleNAR genomics and bioinformatics2021
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed.
- KnowYourCG: Facilitating base-level sparse methylome interpretation.Science advances · 2025Article
- Scalable screening of ternary-code DNA methylation dynamics associated with human traits.Cell genomics · 2025Article
- Placental epigenetic clocks derived from crowdsourcing: Implications for the study of accelerated aging in obstetrics.iScience · 2025Article
- AI-powered precision medicine: utilizing genetic risk factor optimization to revolutionize healthcare.NAR genomics and bioinformatics · 2025Review
- mLiftOver: harmonizing data across Infinium DNA methylation platforms.Bioinformatics (Oxford, England) · 2024Article
- Low-input and single-cell methods for Infinium DNA methylation BeadChips.Nucleic acids research · 2024Article
- Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets.Genome biology · 2023Review
- Who's afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data.Epigenetics & chromatin · 2023Article
- recountmethylation enables flexible analysis of public blood DNA methylation array data.Bioinformatics advances · 2023Article
- Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling.Nature communications · 2022Article
- Saliva cell type DNA methylation reference panel for epidemiological studies in children.EpigeneticsArticle
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
While DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35 360 Illumina Infinium HumanMethylation450K DNAm array samples published on the Gene Expression Omnibus. We learned a controlled vocabulary of sample labels by applying regular expressions to metadata and used existing models to predict various sample properties including epigenetic age. We found approximately two-thirds of samples were from blood, one-quarter were from brain and one-third were from cancer patients. About 19% of samples failed at least one of Illumina's 17 prescribed quality assessments; signal distributions across samples suggest modifying manufacturer-recommended thresholds for failure would make these assessments more informative. We further analyzed DNAm variances in seven tissues (adipose, nasal, blood, brain, buccal, sperm and liver) and characterized specific probes distinguishing them. Finally, we compiled DNAm array data and metadata, including our learned and predicted sample labels, into database files accessible via the recountmethylation R/Bioconductor companion package. Its vignettes walk the user through some analyses contained in this paper.
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.