VISDB 2.0: A comprehensive resource of viral integration sites and their regulatory landscapes in human diseases

The integration of viral DNA into the human genome plays a crucial role in the onset and progression of various diseases, particularly cancers. Such integration events can disrupt host gene regulation, alter chromatin organization, and induce genomic instability. VISDB 2.0 represents a comprehensive and updated version of the original VISDB database, systematically cataloging viral integration sites (VISs) and their functional annotations. This release contains over 270,000 curated VISs from 11 human-associated viruses, encompassing both retroviruses (n = 4) and DNA viruses (n = 7). The data were curated from 209 peer-reviewed publications, representing a 3.5-fold expansion compared to the previous VISDB release. Each integration site has been annotated with genomic context, including target genes, CpG islands, fragile sites, repetitive elements, and key epigenomic features. Folder Overview Virus integration sites (VISs):TSV files providing genomic coordinates and metadata for each viral integration event from 11 human viruses. Target genes:CSV files providing host target genes associated with viral integration events for each virus, including a consolidated list of hotspot genes recurrent across multiple viral species. Drug targets:Text files listing host–virus drug targets for each of the 11 viruses. GO:Pathway enrichment:CSV files containing Gene Ontology and KEGG pathway enrichment analyses of VIS target genes. VIS annotation:Files detailing integration overlaps with CpG islands, fragile sites, and repeat elements within 1 kb and 10 kb flanking regions. VIS motifs:CSV files showing enriched sequence motifs near viral integration sites, identified per virus. Regulatory overlaps:Data describing VISs overlaps with genomic regulatory regions, disease-associated variants, and annotated genomic elements. ncRNA interactions:CSV files listing lncRNA and miRNA interactions associated with each VISs and their target genes.