Evidence map›Paper›PMID 25739977›Full record

ArticleScientific reports2015

Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer.

Yongsheng Li, Yunpeng Zhang, Shengli Li, Jianping Lu, Juan Chen, Yuan Wang, Yixue Li, Juan Xu, Xia Li

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed, 1 pooled it
4.2field-weighted citation impact, top 5% of its field
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

24 citing papers in PubMed, 1 synthesis or guideline pooled it, 61 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 1 institution in 1 country.

Yongsheng LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Yunpeng ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Shengli LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Jianping LuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Juan ChenCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Yuan WangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Yixue Li1] College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China [2] Shanghai Center for Bioinformation Technology, Shanghai, People's Republic of China.
Juan XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Xia LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Harbin Medical University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Despite growing appreciation of the importance of epigenetics in breast cancer, our understanding of epigenetic alterations of non-coding RNAs (ncRNAs) in breast cancer remains limited. Here, we explored the epigenetic patterns of ncRNAs in breast cancers using published sequencing-based methylome data, primarily focusing on the two most commonly studied ncRNA biotypes, long ncRNAs and miRNAs. We observed widely aberrant methylation in the promoters of ncRNAs, and this abnormal methylation was more frequent than that in protein-coding genes. Specifically, intergenic ncRNAs were observed to comprise a majority (51.45% of the lncRNAs and 51.57% of the miRNAs) of the aberrantly methylated ncRNA promoters. Moreover, we summarized five patterns of aberrant ncRNA promoter methylation in the context of genomic CpG islands (CGIs), in which aberrant methylation occurred not only on CGIs, but also in regions flanking CGI and in CGI-lacking promoters. Integration with transcriptional datasets enabled us to determine that the ncRNA promoter methylation events were associated with transcriptional changes. Furthermore, a panel of ncRNAs were identified as biomarkers that discriminated between disease phenotypes. Finally, the potential functions of aberrantly methylated ncRNAs were predicted, suggestiong that ncRNAs and coding genes cooperatively mediate pathway dysregulation during the development and progression of breast cancer.

Indexed as

DNA MethylationEpigenesis, GeneticEpigenomicsGenome-Wide Association StudyBreast NeoplasmsCase-Control StudiesCluster AnalysisCpG IslandsFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansOpen Reading FramesPromoter Regions, GeneticRNA, UntranslatedTranscription Initiation SiteRNA, Untranslated

Identifiers

PMID25739977
PMCPMC4350105
OpenAlexW1989961697

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

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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.