ArticleNucleic acids research2018
The association between copy number aberration, DNA methylation and gene expression in tumor samples.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 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
47 citing papers in PubMed.
- Multi-omics analysis of HLTF context-dependent regulation across TCGA cohorts revealed its potential as new biomarker in tumour.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Identifying High-Dimensional Genomic Factors Modulating Biological Networks Across MultiOmics Data.bioRxiv : the preprint server for biology · 2025Article
- Multimodal analysis of cell-free DNA enhances differentiation of early-stage breast cancer from benign lesions and healthy individuals.BMC biology · 2025Article
- Weight-loss associated DNA methylation patterns: targetable biomarkers and pathway insights.BMC research notes · 2025Article
- Methylation aberrations and genomic instability synergistically drive the evolution of intrahepatic cholangiocarcinoma.Epigenomics · 2025Article
- Benchmarking strategies for CNV calling from whole genome bisulfite data in humans.Computational and structural biotechnology journal · 2025Article
- COL1A1, COL1A2, CHN1, and FN1 Promote Tumorogenesis and Act as Markers of Diagnosis and Survival in Gastric Cancer Patients.Current pharmaceutical biotechnology · 2025Article
- Methods in DNA methylation array dataset analysis: A review.Computational and structural biotechnology journal · 2024Review
- Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation.PLoS computational biology · 2024Article
- Multiomics and machine learning-based analysis of pancancer pseudouridine modifications.Discover oncology · 2024Article
- The DNA methylome of pediatric brain tumors appears shaped by structural variation and predicts survival.Nature communications · 2024Article
- Integrative analysis of genomic and epigenomic regulation reveals miRNA mediated tumor heterogeneity and immune evasion in lower grade glioma.Communications biology · 2024Article
- A study on metabolic characteristics and metabolic markers of gastrointestinal tumors.Cancer biology & therapy · 2023Article
- Article
- Alterations in the Epigenetic Machinery Associated with Prostate Cancer Health Disparities.Cancers · 2023Article
- A revision of the InfiniumPurify R package for genome-wide correction of tumor purity in Infinium DNA methylation array data.Genes & diseases · 2023Article
- CVAM: CNA Profile Inference of the Spatial Transcriptome Based on the VGAE and HMM.Biomolecules · 2023Article
- Six immune-related promising biomarkers may promote hepatocellular carcinoma prognosis: a bioinformatics analysis and experimental validation.Cancer cell international · 2023Article
- Role and mechanism of DNA methylation and its inhibitors in hepatic fibrosis.Frontiers in genetics · 2023Review
- Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes.Molecular biology and evolution · 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
9 authors.
Funding
Abstract
We systematically studied the association between somatic copy number aberration (SCNA), DNA methylation and gene expression using -omic data from The Cancer Genome Atlas (TCGA) on six cancer types: breast cancer, colon cancer, glioblastoma, leukemia, lower-grade glioma and prostate cancer. A major challenge for such integrated study is that the association between DNA methylation and gene expression is severely confounded by tumor purity and cell type composition, which are often unobserved and difficult to estimate. To overcome this challenge, we developed a method to remove confounding effects by calculating the principal components that span the space of the latent factors. Another intriguing findings of our study is that there could be both positive and negative associations between SCNA and DNA methylation, while the CpGs with negative/positive associations with SCNA are often located around CpG islands/ocean, respectively. A joint study of SCNA, DNA methylation, and gene expression suggest that SCNA often affect DNA methylation and gene expression independently.
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.