ArticlePloS one2013
CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers.
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 25 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
25 citing papers in PubMed.
- ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer.BMC medical genomics · 2020Article
- The long non-coding RNAEpigenetics · 2019Article
- Adipokines Deregulate Cellular Communication via Epigenetic Repression ofCancer research · 2019Article
- miR-137 is a tumor suppressor in endometrial cancer and is repressed by DNA hypermethylation.Laboratory investigation; a journal of technical methods and pathology · 2018Article
- Epigenetic silencing of RNF144A expression in breast cancer cells through promoter hypermethylation and MBD4.Cancer medicine · 2018Article
- A Novel Approach for Identifying Relevant Genes for Breast Cancer Survivability on Specific Therapies.Evolutionary bioinformatics online · 2018Review
- Reprimo, a Potential p53-Dependent Tumor Suppressor Gene, Is Frequently Hypermethylated in Estrogen Receptor α-Positive Breast Cancer.International journal of molecular sciences · 2017Article
- Article
- DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database.Nucleic acids research · 2017Review
- NGSmethDB 2017: enhanced methylomes and differential methylation.Nucleic acids research · 2017Article
- Methyl-binding DNA capture Sequencing for Patient Tissues.Journal of visualized experiments : JoVE · 2016Article
- Article
- Genome-wide association studies and epigenome-wide association studies go together in cancer control.Future oncology (London, England) · 2016Article
- Spatiotemporal control of estrogen-responsive transcription in ERα-positive breast cancer cells.Oncogene · 2016Article
- Reprimo as a modulator of cell migration and invasion in the MDA-MB-231 breast cancer cell line.Biological research · 2016Article
- An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line.Journal of Cancer · 2016Article
- Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer.Scientific reports · 2015Article
- Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer.Clinical epigenetics · 2015Article
- DDMGD: the database of text-mined associations between genes methylated in diseases from different species.Nucleic acids research · 2015Article
- PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders.BMC medical genomics · 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
8 authors.
Funding
Abstract
backgroundDNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it possible to find the functional relationship between cancer-specific methylation patterns and their clinicopathological parameters. METHODOLOGY/PRINCIPAL
findingsCancer methylome system (CMS) is a web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. Methylation intensities were obtained from MBDCap-sequencing, pre-processed and stored in the database. 191 patient samples (169 tumor and 22 normal specimen) and 41 breast cancer cell-lines are deposited in the database, comprising about 6.6 billion uniquely mapped sequence reads. This provides comprehensive and genome-wide epigenetic portraits of human breast cancer and endometrial cancer to date. Two views are proposed for users to better understand methylation structure at the genomic level or systemic methylation alteration at the gene level. In addition, a variety of annotation tracks are provided to cover genomic information. CMS includes important analytic functions for interpretation of methylation data, such as the detection of differentially methylated regions, statistical calculation of global methylation intensities, multiple gene sets of biologically significant categories, interactivity with UCSC via custom-track data. We also present examples of discoveries utilizing the framework. CONCLUSIONS/SIGNIFICANCE: CMS provides visualization and analytic functions for cancer methylome datasets. A comprehensive collection of datasets, a variety of embedded analytic functions and extensive applications with biological and translational significance make this system powerful and unique in cancer methylation research. CMS is freely accessible at: http://cbbiweb.uthscsa.edu/KMethylomes/.
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.