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

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 ecc...

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Detalles Bibliográficos
Autores principales: Yang, Min, Qiu, Bo, He, Guo-You, Zhou, Jian-Yuan, Yu, Hao-Jie, Zhang, Yu-Ying, Li, Yan-Shang, Li, Tai-Song, Guo, Jin-Cheng, Li, Xue-Cang, Xie, Jian-Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10112955/
https://www.ncbi.nlm.nih.gov/pubmed/37018146
http://dx.doi.org/10.1093/bioinformatics/btad173
Descripción
Sumario: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.

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