PFusionDB:植物特异性聚变转录的全面数据库
Ajay Arya1, Simran Arora1, Fiza Hamid1
1Bioinformatics Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India.
3 Biotech
|October 31, 2024
概括
这项研究引入了 PFusionDB,这是植物融合转录的新数据库,识别了四种植物中超过20万个独特的融合事件. 该资源通过编目融合转录及其特征来帮助植物研究.
科学领域:
- 植物基因组学和转录基因组学
- 生物信息学和数据库开发
- 分子生物学分子生物学
背景情况:
- 融合转录 (FTs) 是已知的癌症生物标志物,但在植物中尚未得到充分研究.
- 需要为植物FT提供一个全面的资源,以促进该领域的研究.
- 现有的FT识别工具需要适应植物特异性分析.
研究的目的:
- 开发PFusionDB,这是一个新的,植物特定的数据库,用于融合转录.
- 为多种植物物种识别的FT提供一个全面的存储库.
- 为搜索,分析和映射融合成绩单数据提供工具.
主要方法:
- 分析了来自1280个Arabidopsis thaliana,637个Oryza sativa japonica,697个Oryza sativa indica和181个Cicer arietinum样本的RNA-Seq数据.
- 五种不同的工具 (EricScript-Plants,STAR-Fusion,TrinityFusion,SQUID,MapSplice) 用于FT的识别. 这些工具包括:
- 将数据集成到 PFusionDB 平台中,包括开发搜索和对齐模块.
主要成果:
- 在PFusionDB中,有80,170个主机 (A.A. 泰利安纳 (Thaliana),39108 (O.O.) 的人口. 日本植物 (Sativa japonica), 83,330 (O.O.) 种类的植物. 葡萄树 (C. sativa indica) 和 11,500 种 (C. ) 独特的FT.
- 在所有物种中,发现了大量的非经常性FT (单一样本的特征).
- 该数据库包括有关父母基因,结序列,表达水平和基因组坐标的详细信息.
结论:
- PFusionDB是植物融合转录研究的有价值和全面的资源.
- 该数据库促进了植物中FT的探索,支持进一步的功能和进化研究.
- 它为研究人员提供了查询,分析和绘制植物融合成绩单数据的基本工具.
相关概念视频
Transgenic Plants
7.2K
Recombinant DNA technology called transgenesis is often used to add a foreign gene or remove a detrimental gene from an organism. Such genetically modified organisms are called transgenic organisms.
The first-ever transgenic plant was a tobacco plant developed in 1983 that showed resistance against the tobacco mosaic virus. Since then, many transgenic plants have been developed and commercialized for improving the agricultural, ornamental, and horticultural value of a crop plant. Transgenic...
The first-ever transgenic plant was a tobacco plant developed in 1983 that showed resistance against the tobacco mosaic virus. Since then, many transgenic plants have been developed and commercialized for improving the agricultural, ornamental, and horticultural value of a crop plant. Transgenic...
7.2K
Alternative RNA Splicing
21.0K
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
21.0K
Tagging and Fusion Proteins
6.6K
Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
6.6K
Overview of Transposition and Recombination
15.3K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
15.3K
Cell Specific Gene Expression
4.6K
4.6K
RNA-seq
9.8K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.8K


