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

• Published in: Nucleic acids research Vol. 52; no. D1; pp. D1315 - D1326
• Main Authors: Li, Cuidan, Qian, Qiheng, Yan, Chenghao, Lu, Mingming, Li, Lin, Li, Pan, Fan, Zhuojing, Lei, Wenyan, Shang, Kang, Wang, Peihan, Wang, Jie, Lu, Tianyi, Huang, Yuting, Yang, Hongwei, Wei, Haobin, Han, Jingwan, Xiao, Jingfa, Chen, Fei
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 05.01.2024
• Subjects: Atlases as Topic; Endogenous Retroviruses; Humans; Internet Use; Knowledge Bases; Virus Diseases - genetics; Virus Diseases - virology
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkad904

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. Graphical Abstract Graphical Abstract