MethMotif.Org 2024:一个数据库,将特定的转录因子结合动机与DNA甲基化模式集成在一起
Matthew Dyer1, Quy Xiao Xuan Lin2, Sofiia Shapoval1
1Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada.
Nucleic acids research
|October 18, 2023
概括
现在MethMotif提供了700多个转录因子 (TF) 结合配置文件和DNA甲基化数据. 该数据库通过整合人类,小鼠和Arabidopsis.mouse的表观遗传信息和辅因子状态来增强对TF功能的理解.
科学领域:
- 基因组学就是基因组学.
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 生物信息学是一种生物信息学.
背景情况:
- 转录因子 (TFs) 通过DNA结合来调节基因表达.
- DNA甲基化和辅因子相互作用影响TF结合和基因特异性.
- 现有的数据库往往缺乏针对TF结合动机的综合表观遗传和辅因子信息.
研究的目的:
- 增强MethMotif数据库,扩展TF结合概况,DNA甲基化模式和辅因子信息.
- 通过整合表观遗传数据,提供特定环境的TF功能.
- 扩大数据库对多种物种的适用性.
主要方法:
- 扩展了数据库,包括700多个位置重量矩阵 (PWM) 与DNA甲基化概况.
- 基于辅因子和DNA甲基化状态的分离TF结合动机.
- 对人类TF和TF-co-TF复合体的综合预计算基因本体学 (GO) 注释.
- 增加了Mus musculus和Arabidopsis thaliana的数据.
主要成果:
- 更新后的MethMotif数据库包含700多个TF结合基因与相关的DNA甲基化概况.
- 现在TF结合动机根据辅因子和甲基化状态进行分类,从而实现特定上下文的分析.
- 预先计算的GO注释有助于研究TF函数与辅因子和甲基化相关的研究.
- 数据库现在支持人类,老鼠和Arabidopsis.
结论:
- "MethMotif"是第一个将特定上下文的PWM与TF结合动机的表观遗传信息集成的数据库.
- 增强的数据库提供了更深入的洞察力,以特定的背景TF功能和监管机制.
- 扩大物种覆盖范围增加了对更广泛的研究社区的实用性.
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