HervD Atlas: a curated knowledgebase of associations between human endogenous retroviruses and diseases.

Journal: Nucleic acids research
PMID: 37870452

Abstract

Human endogenous retroviruses (HERVs), as remnants of ancient exogenous retrovirus infected and integrated into germ cells, comprise ∼8% of the human genome. These HERVs have been implicated in numerous diseases, and extensive research has been conducted to uncover their specific roles. Despite these efforts, a comprehensive source of HERV-disease association still needs to be added. To address this gap, we introduce the HervD Atlas (https://ngdc.cncb.ac.cn/hervd/), an integrated knowledgebase of HERV-disease associations manually curated from all related published literature. In the current version, HervD Atlas collects 60 726 HERV-disease associations from 254 publications (out of 4692 screened literature), covering 21 790 HERVs (21 049 HERV-Terms and 741 HERV-Elements) belonging to six types, 149 diseases and 610 related/affected genes. Notably, an interactive knowledge graph that systematically integrates all the HERV-disease associations and corresponding affected genes into a comprehensive network provides a powerful tool to uncover and deduce the complex interplay between HERVs and diseases. The HervD Atlas also features a user-friendly web interface that allows efficient browsing, searching, and downloading of all association information, research metadata, and annotation information. Overall, the HervD Atlas is an essential resource for comprehensive, up-to-date knowledge on HERV-disease research, potentially facilitating the development of novel HERV-associated diagnostic and therapeutic strategies.

Authors

  • Cuidan Li
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Qiheng Qian
    National Genomics Data Center of Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  • Chenghao Yan
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Mingming Lu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Lin Li
    Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany.
  • Pan Li
    Department of Infections，Beijing Hospital of Traditional Chinese Medicine, Affiliated to the Capital Medical University, No. 23, Back Road of the Art Gallery, Dongcheng District, Beijing 100010, China.
  • Zhuojing Fan
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Wenyan Lei
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Kang Shang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Peihan Wang
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Jie Wang
  • Tianyi Lu
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Yuting Huang
    Tianjin Medical University Cancer Hospital and Institute, Tianjin, China.
  • Hongwei Yang
    Department of Radiology, Xuanwu Hospital of Capital Medical University, Beijing, China.
  • Haobin Wei
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  • Jingwan Han
    Department of AIDS Research, State Key Laboratory of Pathogen and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
  • Jingfa Xiao
    BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  • Fei Chen
    Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen, China.

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