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Nucleic acids research
Jan 05, 2024;52 (D1): D1072-D1081.

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
Author Information
  1. Shiqi Lin: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  2. Song Wu: University of Chinese Academy of Sciences, Beijing 100049, China. ORCID
  3. Wei Zhao: University of Chinese Academy of Sciences, Beijing 100049, China.
  4. Zhanjie Fang: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  5. Hongen Kang: CAS 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
  6. Xinxuan Liu: CAS 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
  7. Siyu Pan: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  8. Fudong Yu: Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200237, China.
  9. Yiming Bao: University of Chinese Academy of Sciences, Beijing 100049, China.
  10. Peilin Jia: CAS 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
PMID: 37870478 DOI: 10.1093/nar/gkad901

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.

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Grants

  1. XDB38010400/Strategic Priority Research Program of the Chinese Academy of Sciences
  2. 32270706/National Natural Science Foundation of China
  3. 232016009/Startup Research Fund of Henan Academy of Sciences
  4. /Open Biodiversity and Health Big Data Programme of IUBS

MeSH Term

Humans
Chromatin
Genome-Wide Association Study
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Databases, Genetic

Chemicals

Chromatin
Journal Article

Links to CNCB-NGDC Resources

Database Commons: DBC009041 (TargetGene)

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