Table 4.
Information of database for eccDNA study.
| name | availability | modules | application | number of eccDNA | data source | year | reference |
|---|---|---|---|---|---|---|---|
| eccDNAdb | http://www.eccdnadb.org/ | home, browse, search, GB, statistics, submit, external links | enables users to easily determine the biological function and clinical relevance of eccDNAs in human cancers | 1270 (Homo sapiens) | analysis of WGS data from SRA & literature | 2022 | Peng et al. [62] |
| CircleBase | http://circlebase.maolab.org/ | home, search, stats, manual | targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants | 601,036 (Homo sapiens) | literature | 2022 | Zhao et al. [63] |
| eccDNA Atlas | http://lcbb.swjtu.edu.cn/eccDNAatlas | home, browse, search, analysis, statistics, submit | eccDNA annotation (eccDNA regions included in eccDNA Atlas or custom chromatin regions including oncogenes/lncRNAs, typical enhancers, super enhancers, CTCF-binding sites, SNPs, chromatin accessibility and eQTLs), analysis (gene expressions, functions, survival, regulatory network exploring analysis and BLAST) and genome visualization were provided for oncogenes, enhancers, SNPs, chromatin accessibility, etc. | 629,987 eccDNAs, 8221 ecDNAs from literatures and 1105 ecDNAs by AA (Homo sapiens) | literature and analysis of WGS data | 2023 | Zhong et al. [64] |
| eccBase | http://www.eccbase.net | home, browse, search, blast, submission | a total of 50 features were annotated, including basic features, molecular biology properties, and source data. | 754,391 (Homo sapiens) and 481,381 (Mus musculus) | literature curation and public algorithm/database retrieval | 2023 | Sun et al. [65] |
| eccDB | http://www.xiejjlab.bio/eccDB | home, browse, search, analysis, blast, statistics, API | eccDNAs gene expression analysis, survival analysis, GO term functional enrichment analysis, and KEGG pathway annotation, regulatory and epigenetic information annotations for eccDNAs, sequence similarity analysis | 767,981 (Homo sapiens), 372,811 (Mus musculus), 2081 (Saccharomyces cerevisiae), and 174,309 (Arabidopsis) | literature and public algorithm/database retrieval | 2023 | Yang et al. [66] |
| TeCD | http://122.224.251.240:2022 | home, search, blast, statistics, contribute | search and obtain eccDNA data, and analyze the possible potential functions of eccDNA | 193294 (Homo sapiens), 1266 (Saccharomyces cerevisiae), 591 (Arabidopsis thaliana), 434008 (Gallus gallus), 319325 (Mus musculus) | literature | 2023 | Guo et al. [67] |