Evidence map›Paper›PMID 30177244›Full record

ArticleEBioMedicine2018

Capturing functional long non-coding RNAs through integrating large-scale causal relations from gene perturbation experiments.

Jinyuan Xu, Aiai Shi, Zhilin Long, Liwen Xu, Gaoming Liao, Chunyu Deng, Min Yan, Aiming Xie, Tao Luo, Jian Huang and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in EBioMedicine, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing 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

20 citing papers in PubMed.

  1. Article
  2. Review
  3. The Role of Long Intergenic Noncoding RNA in Fetal Development.International journal of molecular sciences · 2024
    Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. The role of LncRNAs in tumor immunotherapy.Cancer cell international · 2023
    Review
  9. Review
  10. Article
  11. Article
  12. Review
  13. Review
  14. Article
  15. Review
  16. Review
  17. Article
  18. Review
  19. Article
  20. Review
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.

Jinyuan XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Aiai ShiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Zhilin LongCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Liwen XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Gaoming LiaoCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Chunyu DengCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Min YanCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Aiming XieCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Tao LuoCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
Jian HuangCenter for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China. Electronic address: hj@uestc.edu.cn.
Yun XiaoCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Harbin, Heilongjiang 150086, China. Electronic address: xiaoyun@ems.hrbmu.edu.cn.
Xia LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Harbin, Heilongjiang 150086, China. Electronic address: lixia@hrbmu.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Characterizing functions of long noncoding RNAs (lncRNAs) remains a major challenge, mostly due to the lack of lncRNA-involved regulatory relationships. A wide array of genome-wide expression profiles generated by gene perturbation have been widely used to capture causal links between perturbed genes and response genes. Through annotating >600 gene perturbation profiles, over 354,000 causal relationships between perturbed genes and lncRNAs were identified. This large-scale resource of causal relations inspired us to develop a novel computational approach LnCAR for inferring lncRNAs' functions, which showed a higher accuracy than the co-expression based approach. By application of LnCAR to the cancer hallmark processes, we identified 38 lncRNAs involved in distinct carcinogenic processes. The "activating invasion & metastasis" related lncRNAs were strongly associated with metastatic progression in various cancer types and could act as a predictor of cancer metastasis. Meanwhile, the "evading immune destruction" related lncRNAs showed significant associations with immune infiltration of various immune cells and, importantly, can predict response to anti-PD-1 immunotherapy, suggesting their potential roles as biomarkers for immune therapy. Taken together, our approach provides a novel way to systematically reveal functions of lncRNAs, which will be helpful for further experimental exploration and clinical translational research of lncRNAs.

Indexed as

Gene Expression ProfilingCell CycleComputational BiologyGene Expression Regulation, NeoplasticHumansImmunityImmunotherapyNeoplasm MetastasisNeoplasmsOpen Reading FramesRNA, Long NoncodingRNA, Long NoncodingCancerFunctionGene perturbationImmunotherapylncRNA

Identifiers

PMID30177244
PMCPMC6156711

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.