Database Commons

a catalog of worldwide biological databases

ViMIC 2.0 is an updated database that provides comprehensively curated data on virus mutations (VMs), viral integration sites (VISs), and multi-omics datasets related to human diseases. Leveraging expanding public data, ViMIC 2.0 significantly enhanced data scale, diversity, and analytical capabilities compared to the previous version. In terms of data volume, the number of virus types has increased from 8 to 28, VM entries have grown from 31 712 to 64 168, virus-related diseases expanded from 77 to 177, literature rose from 2539 to 6433, and omics datasets have substantially increased from 28 sets of single expression profile data to 255 sets of multi-omics data. In addition, ViMIC 2.0 has updated 9409 VISs, 173 048 sequences, newly incorporated sequencing types such as single-cell transcriptomic sequencing (scRNA-seq), and genome binding/occupancy profiling. Regarding the visualization module, ViMIC 2.0 now provides results of differential gene expression analysis for bulk RNA-seq or array, cell type annotation and gene feature plot for scRNA-seq data, and differential methylation analysis for methylation profiling, as well as peak annotation for ChIP-seq/ChIP-on-chip/ATAC-seq data. In summary, ViMIC 2.0 serves as a user-friendly, up-to-date, and well-maintained resource for the virology research community. ViMIC 2.0 is freely accessible at http://www.biomedinfo.cn/ViMIC2.0/index.php.

Molecular mechanisms of virus-related diseases involve multiple factors, including viral mutation accumulation and integration of a viral genome into the host DNA. With increasing attention being paid to virus-mediated pathogenesis and the development of many useful technologies to identify virus mutations (VMs) and viral integration sites (VISs), much research on these topics is available in PubMed. However, knowledge of VMs and VISs is widely scattered in numerous published papers which lack standardization, integration and curation. To address these challenges, we built a pilot database of human disease-related Virus Mutations, Integration sites and Cis-effects (ViMIC), which specializes in three features: virus mutation sites, viral integration sites and target genes. In total, the ViMIC provides information on 31 712 VMs entries, 105 624 VISs, 16 310 viral target genes and 1 110 015 virus sequences of eight viruses in 77 human diseases obtained from the public domain. Furthermore, in ViMIC users are allowed to explore the cis-effects of virus-host interactions by surveying 78 histone modifications, binding of 1358 transcription regulators and chromatin accessibility on these VISs. We believe ViMIC will become a valuable resource for the virus research community. The database is available at http://bmtongji.cn/ViMIC/index.php.