DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins.

Yu-Hao Zeng, Zhen-Ning Yin, Hao Luo, Feng Gao
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Abstract

DNA replication is a complex and crucial biological process in eukaryotes. To facilitate the study of eukaryotic replication events, we present a database of eukaryotic DNA replication origins (DeOri), which collects scattered data and integrates extensive sequencing data on eukaryotic DNA replication origins. With continuous updates of DeOri, the number of datasets in the new release increased from 10 to 151 and the number of sequences increased from 16,145 to 9,742,396. Besides nucleotide sequences and bed files, corresponding annotation files, such as coding sequences (CDS), mRNA, and other biological elements within replication origins, are also provided. The experimental techniques used for each dataset, as well as other statistical data, are also presented on web page. Differences in experimental methods, cell lines, and sequencing technologies have resulted in distinct replication origins, making it challenging to differentiate between cell-specific and non-specific replication. We combined multiple replication origins at the species level, scored them, and screened them. The screened regions were considered as species-conservative origins. They are integrated and presented as reference replication origins (rORIs), including Homo sapiens, Gallus gallus, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans. Additionally, we analyzed the distribution of relevant genomic elements associated with replication origins at the genome level, such as CpG island (CGI), transcription start site (TSS), and G-quadruplex (G4). These analysis results allow users to select the desired data based on it. DeOri is available at http://tubic.tju.edu.cn/deori/.

DeOri 10.0:经实验鉴定的真核生物复制起源的最新数据库。
DNA 复制是真核生物复杂而关键的生物学过程。为了促进对真核生物复制事件的研究,我们建立了真核生物DNA复制起源数据库(DeOri),该数据库收集了真核生物DNA复制起源的零散数据,并整合了大量的测序数据。随着DeOri的不断更新,新版本中的数据集数量从10个增加到151个,序列数量从16,145条增加到9,742,396条。除了核苷酸序列和床文件外,还提供了相应的注释文件,如编码序列(CDS)、mRNA 和复制起源内的其他生物元素。每个数据集所使用的实验技术以及其他统计数据也在网页上提供。实验方法、细胞系和测序技术的不同导致了不同的复制起源,这使得区分细胞特异性复制和非特异性复制具有挑战性。我们在物种水平上结合了多个复制起源,对它们进行了评分和筛选。筛选出的区域被视为物种保守起源。它们被整合为参考复制起源(rORIs),包括智人、斑马鸡、麝鼠、黑腹果蝇和高脚伊蚊。此外,我们还在基因组水平上分析了与复制起源有关的相关基因组元素的分布,如 CpG 岛(CGI)、转录起始位点(TSS)和 G-四叠体(G4)。用户可以根据这些分析结果选择所需的数据。DeOri可在http://tubic.tju.edu.cn/deori/。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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