PFusionDB: a comprehensive database of plant-specific fusion transcripts.

IF 2.6 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

3 Biotech Pub Date : 2024-11-01 Epub Date: 2024-10-28 DOI:10.1007/s13205-024-04132-1

Ajay Arya, Simran Arora, Fiza Hamid, Shailesh Kumar

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引用次数: 0

Abstract

Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of Arabidopsis thaliana, Oryza sativa japonica, Oryza sativa indica, and Cicer arietinum respectively. Here, a total of 76,599 (Arabidopsis thaliana), 35,480 (Oryza sativa japonica), 72,099 (Oryza sativa indica), and 9524 (Cicer arietinum) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04132-1.

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PFusionDB：植物特异性融合转录本综合数据库。

融合转录本（FTs）是众所周知的癌症生物标志物，但在植物中的研究相对不足。在此，我们开发了一个新颖的植物特异性融合转录本数据库 PFusionDB (www.nipgr.ac.in/PFusionDB)。它是一个全面的数据库，分别包含拟南芥、粳稻、籼稻和黑麦的 1280、637、697 和 181 份 RNA-Seq 样本中检测到的 80170、39108、83330 和 11500 个独特融合基因。其中，共有 76599 个融合转录本（拟南芥）、35480 个融合转录本（粳稻）、72099 个融合转录本（籼稻）和 9524 个融合转录本（菊苣）是非重复性的，即只在一个样本中发现。FTs 的鉴定共使用了五种工具，即 EricScript-Plants、STAR-Fusion、TrinityFusion、SQUID 和 MapSplice。在 PFusionDB 中，融合事件的基本信息包括亲代基因信息、连接序列、融合转录本的表达水平、断点坐标、链信息、组织类型、处理信息、融合类型、PFusionDB ID 和序列读取档案（SRA）ID。此外，还有两个搜索模块：此外，还有两个搜索模块："简单搜索 "和 "高级搜索"，以及下载数据的 "浏览 "选项，方便用户使用。另外还有三个不同的模块，即 "BLASTN"、"SW Align "和 "Mapping"，用于有效地将查询序列映射和比对到 FT。PFusionDB 是深入研究错综复杂的植物融合转录本世界的重要资源，为研究人员提供了进一步探索和分析的基础。数据库网址：www.nipgr.ac.in/PFusionDB.Supplementary 信息：在线版本包含补充材料，可查阅 10.1007/s13205-024-04132-1。

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来源期刊

3 Biotech Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

CiteScore

6.00

自引率

0.00%

发文量

314

期刊介绍： 3 Biotech publishes the results of the latest research related to the study and application of biotechnology to: - Medicine and Biomedical Sciences - Agriculture - The Environment The focus on these three technology sectors recognizes that complete Biotechnology applications often require a combination of techniques. 3 Biotech not only presents the latest developments in biotechnology but also addresses the problems and benefits of integrating a variety of techniques for a particular application. 3 Biotech will appeal to scientists and engineers in both academia and industry focused on the safe and efficient application of Biotechnology to Medicine, Agriculture and the Environment.