ASpedia-R:一个包来检索人类替代拼接事件的结合结合特征和基于知识的功能
Daejin Hyung1, Soo Young Cho2, Kyubin Lee3
1Research Institute, National Cancer Center, Goyang, Gyeonggi-do 10408, Republic of Korea.
Bioinformatics advances
|June 3, 2024
概括
替代拼接 (AS) 通过将从DNA到蛋白质的序列特征结合起来来产生遗传多样性. ASpedia-R 软件包分析了这些多基因特征,以了解复杂的基因调节和生物功能.
科学领域:
- 基因组学和分子生物学
- 生物信息学和计算生物学
背景情况:
- 替代拼接 (AS) 是产生人类遗传多样性和表型可塑性的关键机制.
- 异构体和侧面区域包含关键序列特征,包括剪接因子结合位和蛋白质域,这些特征调节异构体的使用和异构体特异性功能.
- 当前的分析工具往往侧重于有限的序列特征,阻碍了对AS监管的全面理解.
研究的目的:
- 开发一个全面的R包,ASpedia-R,用于查询人类基因中的结合结合序列特征.
- 整合多omics数据 (DNA到蛋白质) 和基于知识的拼接信息,以进行AS事件的整体分析.
- 为分析高通量RNA-seq数据和可视化AS相关信息提供一个用户友好的工具.
主要方法:
- 在R.R.中开发ASpedia-R包.
- 收集与AS相关的多种异质多omics数据 (DNA,RNA,蛋白质).
- 基于知识的拼接基因和路径协会的文本挖掘.
- 与AS事件ID转换器集成,用于高吞吐量数据.
- 为结果开发可视化模块 (表格,基因组轨迹,网络,丰富测试).
主要成果:
- ASpedia-R 能够对人类基因的各种结合组合序列特征进行查询.
- 该包整合了多主题数据和路径信息,方便识别关键的AS监管元素.
- 综合的可视化工具允许探索AS事件概况,包括蛋白质-蛋白质相互作用和基因组丰富.
- ASpedia-R通过转换AS事件ID来支持高通量数据分析.
结论:
- ASpedia-R提供了一个方便而强大的平台,以了解替代拼接的全球监管机制.
- 该套件有助于研究多组组序列特征,这些特征对于解释复杂的外型特异生物过程至关重要.
- 通过提供综合分析和可视化,ASpedia-R帮助研究人员破译替代拼接的功能后果.
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