Evidence map›Paper›PMID 37870478›Full record

ArticleNucleic acids research2024

TargetGene: a comprehensive database of cell-type-specific target genes for genetic variants.

Shiqi Lin, Song Wu, Wei Zhao, Zhanjie Fang, Hongen Kang, Xinxuan Liu, Siyu Pan, Fudong Yu, Yiming Bao, Peilin Jia

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Article
  3. Update on the genetics of allergic diseases.The Journal of allergy and clinical immunology · 2025
    Review
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Shiqi LinCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
Song WuUniversity of Chinese Academy of Sciences, Beijing 100049, China.ORCID 0000-0002-0923-639X
Wei ZhaoUniversity of Chinese Academy of Sciences, Beijing 100049, China.
Zhanjie FangCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
Hongen KangCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.ORCID 0000-0002-9581-1329
Xinxuan LiuCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.ORCID 0000-0002-1653-1434
Siyu PanCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
Fudong YuShanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200237, China.
Yiming BaoUniversity of Chinese Academy of Sciences, Beijing 100049, China.
Peilin JiaCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.ORCID 0000-0003-4523-4153

Funding

National Natural Science Foundation of China 32270706Open Biodiversity and Health Big Data Programme of IUBSStartup Research Fund of Henan Academy of Sciences 232016009Strategic Priority Research Program of the Chinese Academy of Sciences XDB38010400
6 · The paper itself

Abstract

Annotating genetic variants to their target genes is of great importance in unraveling the causal variants and genetic mechanisms that underlie complex diseases. However, disease-associated genetic variants are often located in non-coding regions and manifest context-specific effects, making it challenging to accurately identify the target genes and regulatory mechanisms. Here, we present TargetGene (https://ngdc.cncb.ac.cn/targetgene/), a comprehensive database reporting target genes for human genetic variants from various aspects. Specifically, we collected a comprehensive catalog of multi-omics data at the single-cell and bulk levels and from various human tissues, cell types and developmental stages. To facilitate the identification of Single Nucleotide Polymorphism (SNP)-to-gene connections, we have implemented multiple analytical tools based on chromatin co-accessibility, 3D interaction, enhancer activities and quantitative trait loci, among others. We applied the pipeline to evaluate variants from nearly 1300 Genome-wide association studies (GWAS) and assembled a comprehensive atlas of multiscale regulation of genetic variants. TargetGene is equipped with user-friendly web interfaces that enable intuitive searching, navigation and browsing through the results. Overall, TargetGene provides a unique resource to empower researchers to study the regulatory mechanisms of genetic variants in complex human traits.

Indexed as

Databases, GeneticGenome-Wide Association StudyQuantitative Trait LociChromatinHumansPolymorphism, Single NucleotideChromatin

Identifiers

PMID37870478
PMCPMC10767789

What OpenQuestion holds

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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.