CircleBase V2: an eccDNA annotation platform across cancers and species

CircleBase V2 (http://circlebase2.maolab.org) is a comprehensive update of our previously developed database, offering a significantly expanded and functionally enhanced resource for investigating extrachromosomal circular DNA (eccDNA) in human and mouse. This version introduces several key advancements: (i) a 12-fold increase in eccDNA data, comprising over 7.4 million entries from >300 types of cell lines and tissues, providing broader coverage across diverse physiological and disease contexts; (ii) inclusion of mouse eccDNAs, with >3.6 million entries from over 20 tissues, enabling robust cross-species comparative analyses and enhancing translational research with mouse models; (iii) a dedicated motif discovery module that systematically identifies junction-specific sequence patterns, shedding light on molecular mechanisms underlying eccDNA formation; and (iv) an improved functional scoring framework that integrates multi-omic annotations, including chromatin accessibility, regulatory elements, genetic variants, and chromatin interactions, to help prioritize functionally relevant eccDNAs. Additionally, CircleBase V2 features an upgraded user interface with enhanced visualization tools, supporting flexible querying, batch downloads, and integrative analyses. Collectively, these advancements establish CircleBase V2 as an indispensable platform for uncovering the biological roles and regulatory functions of eccDNAs in cancer, development, and other diseases.