Evidence map›Paper›PMID 31525663›Full record

ArticleMolecular therapy. Nucleic acids2019

Comprehensive Characterization of Somatic Mutations Impacting lncRNA Expression for Pan-Cancer.

Yue Gao, Xin Li, Hui Zhi, Yunpeng Zhang, Peng Wang, Yanxia Wang, Shipeng Shang, Ying Fang, Weitao Shen, Shangwei Ning and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular therapy. Nucleic acids, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.

0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed
–field-weighted citation impact
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

22 citing papers in PubMed.

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  11. Designing libraries for pooled CRISPR functional screens of long noncoding RNAs.Mammalian genome : official journal of the International Mammalian Genome Society · 2022
    Review
  12. Article
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  16. The Role ofCancers · 2020
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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

12 authors.

Yue GaoCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Xin LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Hui ZhiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Yunpeng ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Peng WangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Yanxia WangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Shipeng ShangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Ying FangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Weitao ShenCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Shangwei NingCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. Electronic address: ningsw@ems.hrbmu.edu.cn.
Steven Xi ChenDepartment of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA. Electronic address: steven.chen@miami.edu.
Xia LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. Electronic address: lixia@hrbmu.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Somatic mutations have long been recognized as an important feature of cancer. However, analysis of somatic mutations, to date, has focused almost entirely on the protein coding regions of the genome. The potential roles of somatic mutations in human long noncoding RNAs (lncRNAs) are therefore largely unknown, particularly their functional significance across different cancer types. In this study, we characterized some lncRNAs whose expression was affected by somatic mutations (defined as MutLncs) and constructed global MutLnc landscapes across 17 cancer types by systematically integrating multiple levels of data. MutLncs were commonly downregulated and carried low mutation frequencies and non-silent mutations in most cancer types. Co-occurrence analysis in pan-cancer highlighted combined patterns of specific MutLncs, suggesting that a number of MutLncs influence diverse cancer types through combination effects. Several conserved and cancer-specific functions of MutLncs were determined. We further explored the somatic mutations affecting lncRNA expression via mixed and unmixed effects, which led to specific functions in pan-cancer. Survival analysis indicated that MutLncs and co-occurrence pairs can potentially serve as cancer biomarkers. Clarification of the specific roles of MutLncs in human cancers could be beneficial for understanding the molecular pathogenesis of different cancer types and developing the appropriate treatments.

Indexed as

co-occurrencegenelong noncoding RNAsmethylationmicroRNAmixed and unmixed effectspan-cancersomatic mutation

Identifiers

PMID31525663
PMCPMC6745513

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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.