ArticleComparative and functional genomics2012
Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data.
Article in Comparative and functional genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.
- Antipsychotic Medications and DNA Methylation in Schizophrenia and Bipolar Disorder: A Systematic Review.Pharmacotherapy · 2020Pooled it
- An integrative study identifies KCNC2 as a novel predisposing factor for childhood obesity and the risk of diabetes in the Korean population.Scientific reports · 2016Trial
- DNA methylation-mediated suppression of endocytosis confers resistance to duck hepatitis A virus type 3.Microbiology spectrum · 2026Article
- Epigenomic methylome landscape of promoters in vertebrate genomes.bioRxiv : the preprint server for biology · 2026Article
- Promoter Methylation-Expression Coupling of Gliogenesis Genes inInternational journal of molecular sciences · 2026Article
- Aberrant DNA methylation and overexpression of NR0B1 are prognostic biomarkers in KEAP1-mutant lung adenocarcinomas.Discover oncology · 2025Article
- moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks.BMC bioinformatics · 2023Article
- Review
- Obesity-Associated Differentially Methylated Regions in Colon Cancer.Journal of personalized medicine · 2022Article
- Article
- Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072.Journal, genetic engineering & biotechnology · 2021Article
- In silico analysis of promoter regions and regulatory elements (motifs and CpG islands) of the genes encoding for alcohol production in Saccharomyces cerevisiaea S288C and Schizosaccharomyces pombe 972h.Journal, genetic engineering & biotechnology · 2021Article
- Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise.Scientific reports · 2020Article
- Article
- Perspective: Quality Versus Quantity; Is It Important to Assess the Role of Enhancers in Complex Disease from an In Vivo Perspective?International journal of molecular sciences · 2020Article
- Relating gene expression evolution with CpG content changes.BMC genomics · 2014Article
- On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis.BMC genetics · 2014Article
- Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma.BMC systems biology · 2013Article
- Major histocompatibility complex class I core promoter elements are not essential for transcription in vivo.Molecular and cellular biology · 2013Article
- Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel.Human molecular genetics · 2013Article
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 at 3 institutions in 2 countries.
Funding
Abstract
CpG islands are typically located in the 5' end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones' algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.'s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level.
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.