eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species

Abstract

The role of extrachromosomal circular DNA (eccDNA) has been highlighted. More recently, eccDNA-chromosome interactions were identified, suggesting a potential role of eccDNA in transcriptional regulation. Several databases currently provide valuable resources for the study of eccDNAs. However, these databases are primarily focused on Human eccDNAs and do not provide analysis of eccDNA-chromosome interaction and eccDNA gene expression in different tissues. Herein, to further integrate available resources for eccDNA data across multiple species, we developed the eccDB database. The current version of eccDB has collected a total of 1,317,182 eccDNAs in 424 samples from four species (homo sapiens, mus musculus, saccharomyces cerevisiae, and arabidopsis thaliana). eccDB provides regulatory and epigenetic information on eccDNA, including typical enhancers, super-enhancers, transcription factors, DNA methylation positions, risk SNPs, expression quantitative trait locus, chromatin accessibility regions, and chromHMM states. In particular, eccDB provides eccDNAs intrachromosomal and interchromosomal interaction analysis to predict the transcriptional regulatory functions of eccDNA. Moreover, eccDB identifies eccDNAs from unknown DNA sequences and analyzes the functional and evolutionary relationships of an eccDNA 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 eccDNA. eccDB is freely available at http://www.xiejjlab.bio/eccDB .

Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis

“…The rapid advancement of high-throughput sequencing and bioinformatic analysis methods has revealed the extensive prevalence of eccDNA in humans and other species, underscoring the need to establish comprehensive databases. Here, we collated several online databases of eccDNAs, including CircleBase [31] , eccDB [32] , eccDNAdb [11] , eccDNA Atlas [33] , and TeCD [34] . We have documented the annotation and analysis modules offered by each database (as listed in Table 1 ).…”

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

“…To this end, we have processed and are hosting focal amplification calls on AmpliconRepository.org from CCLE, PCAWG and TCGA samples. Indeed, other databases of double minute and ecDNA calls exist [42][43][44][45][46] , however they differ from AmpliconRepository.org in many aspects. While most actually incorporate results from AmpliconSuite-pipeline as a source of ecDNA calls, none provide the complete collection of AmpliconSuite-pipeline outputs associated with the samples.…”

“…While most ecDNA could be assigned to a context class, some remained unknown - highlighting the need to include additional models of formation to our ecDNA context work. At present, this toolset utilizing paired-end short reads has already proven vital to multiple research groups using the methodology to understand the role focal amplifications play across various cancer types, including medulloblastoma 15 , gastric cancer 47 , esophageal cancer 12,13 , head-and-neck cancer 48 , and more 14,49–51 . Identifying and contextualizing genomic alterations mediated by focal amplifications has the potential to improve therapeutic strategy for patients and speed up progress in the identification of new therapeutic targets that exploit the unique properties of focal amplifications.…”

iLEC-DNA: Identifying Long Extra-chromosomal Circular DNA by Fusing Sequence-derived Features of Physicochemical Properties and Nucleotide Distribution Patterns

“…EccDNA sequences are available across various databases such as eccDNA Atlas 66 , TeCD 67 , EccBase 68 , EccDB 69 , and EccDNADB 70 . Each database includes extrachromosomal DNA sequences of different species and cells.…”