ArticlePloS one2013
FastDMA: an infinium humanmethylation450 beadchip analyzer.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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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
13 citing papers in PubMed, 1 synthesis or guideline pooled it, 26 citations in OpenAlex.
- TIGER: The gene expression regulatory variation landscape of human pancreatic islets.Cell reports · 2021Pooled it
- DNA methylation in esophageal cancer: technological advances and early detection clinical applications.Frontiers in oncology · 2025Review
- Differential methylation region detection via an array-adaptive normalized kernel-weighted model.PloS one · 2024Article
- A novel family of beta mixture models for the differential analysis of DNA methylation data: An application to prostate cancer.PloS one · 2024Article
- Pan-cancer analysis of differential DNA methylation patterns.BMC medical genomics · 2020Article
- PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data.BMC bioinformatics · 2019Article
- Integrative molecular analysis of metastatic hepatocellular carcinoma.BMC medical genomics · 2019Article
- A Hybrid Ensemble Approach for Identifying Robust Differentially Methylated Loci in Pan-Cancers.Frontiers in genetics · 2019Article
- Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group.Environmental health perspectives · 2017Article
- Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies.Genome biology · 2017Article
- Establishing an analytic pipeline for genome-wide DNA methylation.Clinical epigenetics · 2016Review
- Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data.Methods (San Diego, Calif.) · 2015Review
- Comprehensive analysis of DNA methylation data with RnBeads.Nature methods · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is vital for many essential biological processes and human diseases. Illumina Infinium HumanMethylation450 Beadchip is a recently developed platform studying genome-wide DNA methylation state on more than 480,000 CpG sites and a few CHG sites with high data quality. To analyze the data of this promising platform, we developed FastDMA which can be used to identify significantly differentially methylated probes. Besides single probe analysis, FastDMA can also do region-based analysis for identifying the differentially methylated region (DMRs). A uniformed statistical model, analysis of covariance (ANCOVA), is used to achieve all the analyses in FastDMA. We apply FastDMA on three large-scale DNA methylation datasets from The Cancer Genome Atlas (TCGA) and find many differentially methylated genomic sites in different types of cancer. On the testing datasets, FastDMA shows much higher computational efficiency than current tools. FastDMA can benefit the data analyses of large-scale DNA methylation studies with an integrative pipeline and a high computational efficiency. The software is freely available via http://bioinfo.au.tsinghua.edu.cn/software/fastdma/.
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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.