IsopretGO-分析和可视化差异拼接的功能后果
Guy Karlebach1, Peter Hansen1, Kristin Köhler2
1The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
NAR genomics and bioinformatics
|December 11, 2024
概括
差异替代拼接 (DAS) 和差异基因表达 (DGE) 在RNA测序 (RNA-seq) 数据中经常显示出不同的功能配置. 我们的新工具isopretGO可视化了这些功能影响,使我们能够识别拼接驱动的功能转变.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 基因本体学过度表示分析 (GO-ORA) 是用于在RNA测序 (RNA-seq) 中对差异表达基因 (DGE) 的特征的标准.
- GO-ORA 不适用于对差异替代拼接 (DAS) 的描述.
- DAS的功能影响仍未得到充分研究.
研究的目的:
- 介绍isopretGO,这是一个桌面应用程序,用于可视化DGE和DAS的功能影响.
- 杆机器学习预测基因本体学 (GO) 对单个异型的注释.
- 能够识别因差异拼接而导致的RNA-seq数据中的功能转移.
主要方法:
- 开发了一个桌面应用程序isopretGO.
- 基于机器学习的集成机器学习对异型的GO注释预测.
- 分析了100个RNA-seq数据集,以比较DGE和DAS的功能概况.
主要成果:
- DAS和DGE经常表现出明显不同的功能配置文件.
- 证明了isopretGO在识别功能转移中的实用性.
- 强调考虑DAS对于全面了解RNA-seq数据的重要性.
结论:
- isopretGO提供了一种新的方法来功能性地表征DAS.
- 对RNA-seq数据的功能分析应考虑DGE和DAS.
- isopretGO促进发现拼接特定的功能洞察力.
相关概念视频
Pre-mRNA Processing: RNA Splicing
5.2K
5.2K
RNA Splicing
56.0K
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
56.0K
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
Chromatin Structure and RNA Splicing
2.7K
2.7K
Gene Duplication and Divergence
6.0K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
6.0K
Pre-mRNA Processing: Modification of pre-mRNA Ends
9.2K
In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
9.2K


