eccDNABase Tutorial

Updated time: April 2025

[1] Overview

Extrachromosomal circular DNA (eccDNA) is a small, circular DNA that detaches from chromosomes and exists in almost all eukaryotic organisms. In human, it is widely distributed in normal tissues, cancer tissues, and body fluids. Recent studies have shown that eccDNA can alter cancer gene expression by gene amplification and gene regulation, and has been considered as a major contributor to the onset of most cancer types and closely related to poor prognosis. It is indispensable to detect the regulatory mechanisms of eccDNA in various complex diseases.

Our database aims to provide a comprehensive and high-quality resource for browsing, searching and analyzing eccDNA from multiple species. Our database contains 1,875,452 eccDNA in 9 species (Homo sapiens, Mouse, Chicken, Arabidopsis thaliana, Rice, Saccharomyces cerevisiae, Tomato, Cow and Amaranthus palmeri), 63 diseases (including cancers, HIV infectious disease, type 2 diabetes mellitus, cerebrovascular diseases and so on) and healthy human from PubMed literatures. Each entry provides detailed information, including eccDNA ID, type, chromosomal localization, species, tissue or cell line source, disease name and Disease Ontology ID, overlap length and percentage with genes, oncogene overlap, detection method, and links to literature and source databases
Our database is unique in several ways::
  • (i) compared to published eccDNA databases, our database contains the highest amount of eccDNA entries, spanning across the most species and diseases;
  • (ii) we integrate the latest published literature on eccDNA data;
  • (iii)Each eccDNA entry in the database contains highly detailed information, including the eccDNA type, oncogene annotations, and clear sample source and data source. Additionally, the database provides a comprehensive analysis of the gene overlaps based on both the hg19 and hg38 genome versions, including the overlap percentage of genes and the overlap percentage of eccDNA. These thorough annotations and analyses ensure high precision and reliability of the data, greatly enhancing the depth of eccDNA research and its biomedical applications.

[2] Browse

To browse eccDNA association data in the database, please select the menu "Browse". Users can browse all the entries for different species in three ways: by eccDNA location, by gene or by disease.

[3] Search

To search data in the database, please select the menu "Search".

In the eccDNABase database, users can search all entries in three ways: by eccDNA location, by gene, or by disease . Detailed information shown in search results:

[4] Download

To download data in the database, please select the menu "Download". The eccDNABase provides two downloadable file ( Homo sapiens or other species ).

[5] Submit

To submit data in the database, please select the menu "Submit". We will also encourage research scientists to submit the eccDNA association. The users need to input their data into corresponding blanks and then submit the query. The submitted information in the future will be manually reviewed and then integrated into this database.

[6] Question and Answer

If you have any questions, suggestions and comments, please feel free to contact Dr. Zheng Zhao at zhaozheng0503@ccmu.edu.cn