Evidence map›Paper›PMID 40847441›Full record

ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2025

Interpretation of RNA Universe and Coding Potential Using IntRNA.

Yunxia Wang, Minjie Mou, Shijie Huang, Wei Zhang, Ziqi Pan, Jing Tang, Yihao Wang, Qingxia Yang, Feng Zhu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Article
  2. 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

9 authors.

Yunxia WangCollege of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou, 310058, China.
Minjie MouCollege of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou, 310058, China.
Shijie HuangCollege of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou, 310058, China.
Wei ZhangCollege of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou, 310058, China.
Ziqi PanCollege of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou, 310058, China.
Jing TangCollege of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China.
Yihao WangThe High School Affiliated to Renmin University of China, No. 37 Zhongguancun Street. Haidian District, Beijing, 100080, China.
Qingxia YangZhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
Feng ZhuCollege of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou, 310058, China.ORCID https://orcid.org/0000-0001-8069-0053

Funding

National Key R&D Programs of China 2024YFA1307503National Natural Science Foundation of China 82373790 22220102001 62201289Natural Science Foundation of Zhejiang RG25H300001
6 · The paper itself

Abstract

The interpretation of RNA universe and coding potential are long-standing issues in modern RNA studies, and three crucial questions remain unanswered: a) how to detect and interpret the coding potential of RNA, b) how to annotate the sophisticated taxonomy of the sncRNAs, and c) how to successfully distinguish between circular and linear lncRNAs. In this study, a multi-channel deep learning framework, IntRNA, is thus constructed to interpret RNA universe and coding potential. First, a large number of RNA encoding features are proposed, which dramatically enlarged the available feature space. Second, a method realizing image-like representation of RNA sequences is developed to describe the intrinsic correlation among the encoding features generated above. Third, a dual-path model is constructed, which consistently performed the best among existing methods in various benchmarks. IntRNA's interpretability is also validated by analysis, and all source codes are accessible at: https://idrblab.org/intrna/ and https://github.com/idrblab/intrna.

Indexed as

Computational BiologyDeep LearningRNARNA, Long NoncodingHumansRNA, CircularSequence Analysis, RNARNARNA, CircularRNA, Long Noncodingcoding potentialdeep learningRNA annotationRNA representationRNA universe

Identifiers

PMID40847441
PMCPMC12631819

What OpenQuestion holds

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LicenceCC BY
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.