ViMIC: A Database of Human Disease-related Virus Mutations, Integration Sites and Cis-effects

Abstract

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), abundant literatures on these topics are available in PubMed. However, knowledge of VMs and VISs is widely scattered in numerous published papers, and the association of VMs with VISs in the viral genome or the functional annotation of VISs still lacks integration and curation. To address these challenges, we built a database of human disease-related Virus Mutations, Integration sites and Cis-effects (ViMIC), which specialize in three features: virus mutation sites, viral integration sites and target genes. In total, the ViMIC provides information on 6,461 VMs, 79,089 VISs, and 15,056 viral target genes of 8 viruses in 65 human diseases obtained from literatures. Furthermore, in ViMIC, users are allowed to explore the cis-effects of virus-host interactions by surveying 78 histone modifications, binding of 1,358 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.

Deep Sequencing of HPV16 E6 Region Reveals Unique Mutation Pattern of HPV16 and Predicts Cervical Cancer

“…In this study, we found that the D32E and H85Y variants exhibited a significantly higher ability to degrade p53 compared to the E6 wild type for first time ( P < 0.05). However, it is noteworthy that, the same as the previous studies ( 18 , 38 ), the mutation frequency of H85Y is higher in NHSIL patients, indicating that additional mechanisms may be involved in the epithelial transformation process.…”

Validation of the GALAD model for early diagnosis and monitoring of hepatocellular carcinoma in Chinese multicenter study

“…Globally, approximately 350 million people are infected with HBV, and 20%‐30% of chronically HBV‐infected individuals may develop cirrhosis and HCC 33,34 . About 80% of HCC cases are related to HBV infection in China 35 .…”

ViMRT: a text-mining tool and search engine for automated virus mutation recognition

“…The gold standard file of virus mutation was collected from our previously developed ViMIC database (Wang et al, 2022), consisting of mutation-related literature in five viruses, HBV, HIV, human papillomavirus (HPV), human T-cell lymphotropic virus type-1 (HTLV1) and Epstein-Barr virus. In this study, the positive samples consisted of 1246 abstracts containing virus mutation information.…”

“…Furthermore, due to the inconsistency of virus mutations and the lack of standard mutation nomenclature, the conventional 'Keyword Search' may be difficult to quickly and non-redundantly get desired mutation information from literature in PubMed. As such, extracting, mining and integrating virus mutation-related information from those extremely large amounts of literature has become an increasingly important task in many downstream applications, such as virus mutation database development (Davey et al, 2014;Wang et al, 2022), immune V C The Author(s) 2022. Published by Oxford University Press.…”