eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species
Min Yang, Bo Qiu, Guoyou He, Jianyuan Zhou, Haojie Yu, Yuying Zhang, Yan-Shang Li, Tai-Song Li, Jincheng Guo, Xuecang Li, Jian‐Jun Xie
Abstract
SUMMARY: We developed the eccDB database to integrate available resources for extrachromosomal circular DNA (eccDNA) data. eccDB is a comprehensive repository for storing, browsing, searching, and analyzing eccDNAs from multispecies. The database provides regulatory and epigenetic information on eccDNAs, with a focus on analyzing intrachromosomal and interchromosomal interactions to predict their transcriptional regulatory functions. Moreover, eccDB identifies eccDNAs from unknown DNA sequences and analyzes the functional and evolutionary relationships of eccDNAs among different species. Overall, eccDB offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher the molecular regulatory mechanisms of eccDNAs. AVAILABILITY AND IMPLEMENTATION: eccDB is freely available at http://www.xiejjlab.bio/eccDB.