GPS:一个用户友好的网络应用程序,以帮助优先考虑功能基因和变异,基于基因组范围的关联研究的证据
Kira J Stanzick1, Klaus J Stark1, Mathias Gorski1
1Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.
BMC bioinformatics
|September 22, 2023
概括
GPS是一种新的网络工具,可以让研究人员轻松访问功能上的遗传数据. 它有助于将遗传发现转化为潜在的新病治疗方法.
科学领域:
- 遗传学和生物信息学 遗传学和生物信息学
- 科研究 科研究
- 计算生物学 计算生物学
背景情况:
- 全基因组关联研究 (GWAS) 已经确定了许多与功能相关的遗传位置.
- 将GWAS发现与GWAS后分析 (例如,精细映射,注释) 整合起来,可以产生病病因学和生理学的假设.
- 将这些遗传见解转化为可操作的研究,例如识别治疗点,需要为没有专门GWAS专业知识的研究人员提供可访问的数据呈现.
研究的目的:
- 介绍 KidneyGPS,一个用户友好的网络应用程序,旨在整合和呈现基因关联数据估计的膜过率 (eGFR).
- 整合多样化的GWAS后信息,包括SNP到基因映射,基因到表型数据和基因可转换性,以促进假设生成和目标识别.
- 根据遗传证据,为脏研究人员提供一个可访问的平台,以探索和优先考虑与功能相关的基因.
主要方法:
- 脏GPS集成了来自慢性病遗传学联盟的eGFR遗传变异关联数据.
- 它包含功能/调控注释,脏特异性基因表型 (人/小鼠) 和基因可用性信息.
- 该应用程序使用RShiny进行模块化实现,实现简单的更新,并提供基因,变异和区域的搜索功能,以及可自定义的基因优先级 (GPS) 选项卡.
主要成果:
- 脏GPS总结了5906个基因在424个eGFR GWAS位点和35885个变异在594个独立信号中的证据.
- 该平台提供了直观的搜索功能和一个"GPS选项卡",用于根据用户定义的标准生成优先级的基因列表.
- 它提供了关于功能相关的遗传关联和功能注释的全面概述.
结论:
- 脏GPS解决了一般GWAS平台和脏研究人员的特定需求之间的差距.
- 它通过提供聚焦的,可访问的数据,促进了将in silico遗传发现转化为体外或体内研究.
- 该平台是推动脏研究和确定潜在治疗策略的宝贵资源.
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