基因特异结合 (ASB) 分析仪用于对基因特异结合SNP的注释
Ying Li1, Xiao-Ou Zhang1, Yan Liu1
1Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200010, China.
BMC bioinformatics
|December 8, 2023
概括
ASB-分析仪识别了基因特异结合 (ASB) SNPs,揭示了序列变异如何影响转录因子结合和疾病风险. 这个用户友好的工具有助于从测序数据中检测和描述ASB事件.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 分子生物学分子生物学
背景情况:
- 当转录因子 (TFs) 偏好地与异构性单核酸多态 (SNP) 的一个等位基结合时,发生了等位基特定结合 (ASB).
- ASB事件可以阐明遗传变异对TF结合的功能影响.
- 这些事件可能对理解疾病易感性有影响.
研究的目的:
- 开发和介绍ASB-analyzer,这是一个用于有效分析ASB事件的软件平台.
- 将ASB SNP识别,注释,动机分析和表型关联集成到一个管道中.
- 为ASB SNPs的检测,表征和可视化提供一个用户友好的工具.
主要方法:
- ASB-分析器处理原始测序数据以生成ASB SNP及其表型的报告.
- 该平台集成了细胞遗传映射,生物注释,动机分析和表型关联.
- 分析涉及三十个GM12878 ChIP-seq数据集.
主要成果:
- 从30个GM12878 ChIP-seq数据集中确定了3772个ASB SNPs.
- 证明了ASB SNP在关键的TF绑定领域中得到了丰富.
- ASB-分析器有助于快速有效地生成ASB SNP报告.
结论:
- ASB-analyzer是一个开源的,用户友好的工具,用于检测,描述和可视化ASB SNP.
- 该工具以Python,R和bash shell实现,包装在Conda环境中.
- 在GitHub上提供,促进可访问性和协作研究.
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