Trial reportThe American journal of pathology2013
Whole-genome methylation sequencing reveals distinct impact of differential methylations on gene transcription in prostate cancer.
Trial report in The American journal of pathology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 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
39 citing papers in PubMed, 54 citations in OpenAlex.
- NNMT Loss Drives Cancer Progression by enhancing SAM availability for mTORC1 Signaling and Chromatin Methylation.bioRxiv : the preprint server for biology · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- Deep spatial sequencing revealing differential immune responses in human hepatocellular carcinoma.Frontiers in cell and developmental biology · 2025Article
- Utility analyses of AVITI sequencing chemistry.BMC genomics · 2024Article
- Immuno-targeting the ectopic phosphorylation sites of PDGFRA generated by MAN2A1-FER fusion in HCC.Hepatology communications · 2024Article
- Serum Fusion Transcripts to Assess the Risk of Hepatocellular Carcinoma and the Impact of Cancer Treatment through Machine Learning.The American journal of pathology · 2024Article
- Utility Analyses of AVITI Sequencing Chemistry.bioRxiv : the preprint server for biology · 2024Article
- Review
- Article
- DNA methylation biomarkers distinguishing early-stage prostate cancer from benign prostatic hyperplasia.Prostate international · 2023Article
- DNA Methylation Landscapes of Prostate Cancer Brain Metastasis Are Shaped by Early Driver Genetic Alterations.Cancer research · 2023Article
- Fusion Gene Detection in Prostate Cancer Samples Enhances the Prediction of Prostate Cancer Clinical Outcomes from Radical Prostatectomy through Machine Learning in a Multi-Institutional Analysis.The American journal of pathology · 2023Article
- Recent advances in understanding DNA methylation of prostate cancer.Frontiers in oncology · 2023Review
- The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.Cancer research · 2022Article
- Dynamic expression of SNAI2 in prostate cancer predicts tumor progression and drug sensitivity.Molecular oncology · 2022Article
- HOXB13 suppresses de novo lipogenesis through HDAC3-mediated epigenetic reprogramming in prostate cancer.Nature genetics · 2022Article
- Androgen receptor and MYC equilibration centralizes on developmental super-enhancer.Nature communications · 2021Article
- Detection of fusion gene transcripts in the blood samples of prostate cancer patients.Scientific reports · 2021Article
- Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer.Nature communications · 2021Article
- Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer.BioMed research international · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
DNA methylation is one of the most important epigenetic mechanisms in regulating gene expression. Genome hypermethylation has been proposed as a critical mechanism in human malignancies. However, whole-genome quantification of DNA methylation of human malignancies has rarely been investigated, and the significance of the genome distribution of CpG methylation is unclear. We performed whole-genome methylation sequencing to investigate the methylation profiles of 13 prostate samples: 5 prostate cancers, 4 matched benign prostate tissues adjacent to tumor, and 4 age-matched organ-donor prostate tissues. Alterations of methylation patterns occurred in prostate cancer and in benign prostate tissues adjacent to tumor, in comparison with age-matched organ-donor prostates. More than 95% alterations of genome methylation occurred in sequences outside CpG islands. Only a small fraction of the methylated CpG islands had any effect on RNA expression. Both intragene and promoter CpG island methylations negatively affected gene expression. However, suppressions of RNA expression did not correlate with levels of CpG island methylation, suggesting that CpG island methylation alone might not be sufficient to shut down gene expression. Motif analysis revealed a consensus sequence containing Sp1 binding motif significantly enriched in the effective CpG islands.
Indexed as
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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.