ArticleGenome biology2014
Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5, and EOMES in human hepatocellular carcinoma.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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
41 citing papers in PubMed, 60 citations in OpenAlex.
- Antidepressant effects of Gardeniae Fructus on chronic unpredictable mild stress model mice: involvement of DNMT3B-mediated epigenetic regulation of GR in the prefrontal cortex.Journal of natural medicines · 2026Article
- Serpina3c protects against metabolic dysfunction-associated steatotic liver disease in offspring induced by prenatal prednisone exposure.Signal transduction and targeted therapy · 2026Article
- Article
- Discovery of novel diagnostic biomarkers of hepatocellular carcinoma associated with immune infiltration.Annals of medicine · 2025Article
- ECM1 expression in chronic liver disease: Regulation by EGF/STAT1 and IFNγ/NRF2 signalling.JHEP reports : innovation in hepatology · 2025Article
- Hederasaponin C ameliorates chronic obstructive pulmonary disease pathogenesis by targeting TLR4 to inhibit NF-κB/MAPK signaling pathways.Chinese medicine · 2025Article
- Ten-Eleven Translocation Family Proteins: Structure, Biological Functions, Diseases, and Targeted Therapy.MedComm · 2025Review
- Identifying potential signatures of immune cells in hepatocellular carcinoma using integrative bioinformatics approaches and machine-learning strategies.Immunologic research · 2025Article
- ART altered DNA methylation of the imprinted gene H19 in fetal tissue after multifetal pregnancy reduction.Journal of assisted reproduction and genetics · 2024Article
- TET2-mediated ECM1 hypomethylation promotes the neovascularization in active proliferative diabetic retinopathy.Clinical epigenetics · 2024Article
- Differential gene screening and bioinformatics analysis of epidermal stem cells and dermal fibroblasts during skin aging.Scientific reports · 2022Article
- Impact of Exercise and Aging on Mitochondrial Homeostasis in Skeletal Muscle: Roles of ROS and Epigenetics.Cells · 2022Review
- Advancements in Activating Transcription Factor 5 Function in Regulating Cell Stress and Survival.International journal of molecular sciences · 2022Review
- Translational and post-translational control of human naïve versus primed pluripotency.iScience · 2022Article
- Screening and analysis of RNAs associated with activated memory CD4 and CD8 T cells in liver cancer.World journal of surgical oncology · 2022Article
- Identification of Signature Genes in the PD-1 Relative Gastric Cancer Using a Combined Analysis of Gene Expression and Methylation Data.Journal of oncology · 2022Article
- Identification and validation of DNA methylation markers to predict axillary lymph node metastasis of breast cancer.PloS one · 2022Article
- Tumor Suppressor 4.1N/Frontiers in genetics · 2022Article
- Low expression of RalGAPs associates with the poorer overall survival of head and neck squamous cell carcinoma.Translational cancer research · 2021Article
- A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing.Briefings in bioinformatics · 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
13 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDifferences in 5-hydroxymethylcytosine, 5hmC, distributions may complicate previous observations of abnormal cytosine methylation statuses that are used for the identification of new tumor suppressor gene candidates that are relevant to human hepatocarcinogenesis. The simultaneous detection of 5-methylcytosine and 5-hydroxymethylcytosine is likely to stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma.
resultsHere, we performed ultra-performance liquid chromatography/tandem mass spectrometry and single-base high-throughput sequencing, Hydroxymethylation and Methylation Sensitive Tag sequencing, HMST-seq, to synchronously measure these two modifications in human hepatocellular carcinoma samples. After identification of differentially methylated and hydroxymethylated genes in human hepatocellular carcinoma, we integrate DNA copy-number alterations, as determined using array-based comparative genomic hybridization data, with gene expression to identify genes that are potentially silenced by promoter hypermethylation.
conclusionsWe report a high enrichment of genes with epigenetic aberrations in cancer signaling pathways. Six genes were selected as tumor suppressor gene candidates, among which, ECM1, ATF5 and EOMES are confirmed via siRNA experiments to have potential anti-cancer functions.
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.