Science Bulletin, 25 December, 2024, DOI：https://doi.org/10.1016/j.scib.2024.12.030

TOAnnoPriDB: an integrative database for trans-omic annotation and prioritization of non-coding variants across human genome

Tingrui Song, Yirong Shi, Yanyan Li, Di Hao, Kaixin Zhan, Tao Xu, Runsheng Chen, Shunmin He

Abstract

Genetic variants in the non-coding regions of the genome can significantly influence gene expression and regulation through various mechanisms, including altering transcription factor (TF) binding, histone modifications, and chromatin accessibility. These mechanisms are increasingly recognized as playing crucial roles in the development of complex diseases. To comprehensively understand the functional impact of non-coding variants, it is essential to integrate genomic, transcriptomic, epigenomic, and proteomic data. The advent of high-throughput sequencing technologies and the availability of large-scale genomic, transcriptomic, proteomics and epigenomic data have greatly facilitated the annotation and interpretation of non-coding variants from a trans-omics perspective, enabling a more comprehensive understanding of their functional consequences. However, most current studies examining the effects of genetic variants rely on data from a single or limited number of layers, such as GREEN-DB (primarily focuses on regulatory), GWAVA (based on ENCODE/GENCODE, evolutionary conservation and GC-content), RegulomeDB (seven data types including TF binding sites, chromatin states, TF motifs, Footprints, eQTLs and caQTLs), etc.

Article link：https://www.sciencedirect.com/science/article/pii/S209592732400937X?via%3Dihub