Evidence map›Paper›PMID 41099605›Full record

ArticleNucleic acids research2026

LnCeVar 2.0: an updated resource and web tools for genomic variations disrupting ceRNA networks from single-cell/spatial transcriptomics data.

Qiuyan Guo, Qian Liu, Mengyu Xin, Houxing Li, Jiatong Li, Yifan Dai, Rui Sun, Yujie Zhang, Yuting He, Borui Xu and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

15 authors.

Qiuyan GuoDepartment of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin 150081, China.
Qian LiuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Mengyu XinCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Houxing LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Jiatong LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Yifan DaiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Rui SunCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Yujie ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Yuting HeCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Borui XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Xinxin ShanCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Yue GaoCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Shangwei NingCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0000-0003-4079-8945
Hui ZhiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0000-0001-9103-8642
Peng WangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.ORCID 0000-0002-5716-9937

Funding

Harbin Medical University 2024JQ20Heilongjiang Provincial Natural Science Foundation YQ2024H013National Natural Science Foundation of China 82373408National Natural Science Foundation of China 82573333National Natural Science Foundation of China 82573599
6 · The paper itself

Abstract

LnCeVar 2.0 (available at http://bio-bigdata.hrbmu.edu.cn/LnCeVar or http://www.bio-bigdata.net/LnCeVar) is an updated database investigating genomic variations that disrupt competing endogenous RNA (ceRNA) networks via single-cell and spatial transcriptomics. Enhancements include expanded data and improved features: (i) 16 937 experimentally supported cancer biomarkers as well as 5785 validated ceRNA interactions and single nucleotide variant (SNV)-ceRNA events, manually curated and linked to key cancer pathogenic processes; (ii) 812 single-cell RNA sequencing/spatial transcriptomics RNA sequencing datasets covering 102 diseases, clinical treatments (e.g. chemotherapy, immunotherapy), and normal tissues; (iii) 5 218 062 single-cell- and spatial-specific SNV-ceRNA events across 2 673 603 cells/spots, with cellular functional perturbation networks; (iv) 5 comprehensive and 12 mini tools for multilevel cross talk analysis and 3D visualization; and (v) novel inference of SNV effects on cell types, states, and functions at single-cell and spatial levels. LnCeVar 2.0 features a user-friendly interface for searching, browsing, and analyzing data. For instance, the CeVarState interface illustrates how SNV-ceRNA events influence cell states during developmental processes, revealing interactions that determine cell fate. The CeVarSC3D and CeVarST3D tools perform multilevel cross talk analyses of SNVs, ceRNA networks, and cell states in disease pathology, providing interactive 3D visualizations. Overall, we anticipate that the updated database will facilitate the high-resolution investigation of SNV-ceRNA networks and advance our understanding of the regulatory mechanisms in complex disease ecosystems.

Indexed as

Databases, GeneticGene Regulatory NetworksSoftwareTranscriptomeGene Expression ProfilingGenomicsHumansInternetNeoplasmsPolymorphism, Single NucleotideRNA, Competitive EndogenousSequence Analysis, RNASingle-Cell AnalysisRNA, Competitive Endogenous

Identifiers

PMID41099605
PMCPMC12807714

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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.