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TeCD:染色体外环状 DNA 集合数据库。

TeCD: The eccDNA Collection Database for extrachromosomal circular DNA.

机构信息

Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013, China.

Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013, China.

出版信息

BMC Genomics. 2023 Jan 27;24(1):47. doi: 10.1186/s12864-023-09135-5.


DOI:10.1186/s12864-023-09135-5
PMID:36707765
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9881285/
Abstract

BACKGROUND: Extrachromosomal circular DNA (eccDNA) is a kind of DNA that widely exists in eukaryotic cells. Studies in recent years have shown that eccDNA is often enriched during tumors and aging, and participates in the development of cell physiological activities in a special way, so people have paid more and more attention to the eccDNA, and it has also become a critical new topic in modern biological research. DESCRIPTION: We built a database to collect eccDNA, including animals, plants and fungi, and provide researchers with an eccDNA retrieval platform. The collected eccDNAs were processed in a uniform format and classified according to the species to which it belongs and the chromosome of the source. Each eccDNA record contained sequence length, start and end sites on the corresponding chromosome, order of the bases, genomic elements such as genes and transposons, and other information in the respective sequencing experiment. All the data were stored into the TeCD (The eccDNA Collection Database) and the BLAST (Basic Local Alignment Search Tool) sequence alignment function was also added into the database for analyzing the potential eccDNA sequences. CONCLUSION: We built TeCD, a platform for users to search and obtain eccDNA data, and analyzed the possible potential functions of eccDNA. These findings may provide a basis and direction for researchers to further explore the biological significance of eccDNA in the future.

摘要

背景:染色体外环状 DNA(eccDNA)是一种广泛存在于真核细胞中的 DNA。近年来的研究表明,eccDNA 在肿瘤和衰老过程中常常富集,并以特殊的方式参与细胞生理活动的发展,因此人们越来越关注 eccDNA,它也成为现代生物研究的一个关键新课题。

描述:我们构建了一个数据库来收集 eccDNA,包括动物、植物和真菌,并为研究人员提供了一个 eccDNA 检索平台。收集到的 eccDNAs 以统一的格式进行处理,并根据所属物种和来源染色体进行分类。每个 eccDNA 记录包含序列长度、对应染色体上的起始和结束位点、碱基顺序、基因和转座子等基因组元件以及各自测序实验中的其他信息。所有数据都存储在 TeCD(The eccDNA Collection Database)中,并在数据库中添加了 BLAST(Basic Local Alignment Search Tool)序列比对功能,用于分析潜在的 eccDNA 序列。

结论:我们构建了 TeCD,一个供用户搜索和获取 eccDNA 数据的平台,并分析了 eccDNA 的潜在功能。这些发现可能为研究人员未来进一步探索 eccDNA 的生物学意义提供基础和方向。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/23224e07a55f/12864_2023_9135_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/9860e8482b4b/12864_2023_9135_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/2d122b1282d3/12864_2023_9135_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/9882fc46d469/12864_2023_9135_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/1a8f5a8122df/12864_2023_9135_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/74492aba0d85/12864_2023_9135_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/30870927dfa9/12864_2023_9135_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/23224e07a55f/12864_2023_9135_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/9860e8482b4b/12864_2023_9135_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/2d122b1282d3/12864_2023_9135_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/9882fc46d469/12864_2023_9135_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/1a8f5a8122df/12864_2023_9135_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/74492aba0d85/12864_2023_9135_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/30870927dfa9/12864_2023_9135_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5277/9881285/23224e07a55f/12864_2023_9135_Fig7_HTML.jpg

相似文献

[1]
TeCD: The eccDNA Collection Database for extrachromosomal circular DNA.

BMC Genomics. 2023-1-27

[2]
Characterization of extrachromosomal circular DNA in cattle using 676 whole genome sequencing datasets.

Anim Genet. 2022-12

[3]
eccDNA Atlas: a comprehensive resource of eccDNA catalog.

Brief Bioinform. 2023-3-19

[4]
Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants.

Curr Opin Plant Biol. 2022-10

[5]
The characteristics of extrachromosomal circular DNA in patients with end-stage renal disease.

Eur J Med Res. 2023-3-27

[6]
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data.

BMC Bioinformatics. 2022-1-14

[7]
CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.

Brief Bioinform. 2022-11-19

[8]
Extrachromosomal circular DNA: a new potential role in cancer progression.

J Transl Med. 2021-6-10

[9]
Extrachromosomal circular DNA: Current status and future prospects.

Elife. 2022-10-18

[10]
eccDNAdb: a database of extrachromosomal circular DNA profiles in human cancers.

Oncogene. 2022-5

引用本文的文献

[1]
Extrachromosomal Circular DNA in Cancer: Mechanisms and Clinical Applications.

Cell Prolif. 2025-6

[2]
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse.

Database (Oxford). 2024-12-18

[3]
Exploring the potential of extrachromosomal DNA as a novel oncogenic driver.

Sci China Life Sci. 2025-1

[4]
Decoding the genomic enigma: Approaches to studying extrachromosomal circular DNA.

Heliyon. 2024-8-20

[5]
Bioinformatics advances in eccDNA identification and analysis.

Oncogene. 2024-10

[6]
Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer.

Biomolecules. 2024-4-17

[7]
Long extrachromosomal circular DNA identification by fusing sequence-derived features of physicochemical properties and nucleotide distribution patterns.

Sci Rep. 2024-4-24

[8]
Mobile circular DNAs regulating memory and communication in CNS neurons.

Front Mol Neurosci. 2023-12-6

[9]
Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications.

Genes (Basel). 2023-6-20

[10]
Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis.

Comput Struct Biotechnol J. 2023-5-18

本文引用的文献

[1]
eccDNAdb: a database of extrachromosomal circular DNA profiles in human cancers.

Oncogene. 2022-5

[2]
CircleBase: an integrated resource and analysis platform for human eccDNAs.

Nucleic Acids Res. 2022-1-7

[3]
Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer.

Mol Cancer. 2021-9-3

[4]
Extrachromosomal circular DNA: a new potential role in cancer progression.

J Transl Med. 2021-6-10

[5]
Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer.

Int J Biol Sci. 2021

[6]
Deciphering extrachromosomal circular DNA in Arabidopsis.

Comput Struct Biotechnol J. 2021-2-9

[7]
The Dfam community resource of transposable element families, sequence models, and genome annotations.

Mob DNA. 2021-1-12

[8]
Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance.

J Hematol Oncol. 2020-9-14

[9]
ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines.

Sci Adv. 2020-5

[10]
The EccDNA Replicon: A Heritable, Extranuclear Vehicle That Enables Gene Amplification and Glyphosate Resistance in .

Plant Cell. 2020-7

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