Regulatory Landscape Enrichment Analysis (RLEA) using gaiaAssociation.
Regulatory Landscape Enrichment Analysis (RLEA) using gaiaAssociation.
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使用 gaiaAssociation 进行监管景观富集分析 (RLEA)。
DOI：
10.1101/2023.10.11.561933
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Greally,JohnM
中科院分区：
文献类型：
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作者：
Sosa,EricA;Rosean,Samuel;O'Shea,Dónal;Raj,SrilakshmiM;Seoighe,Cathal;Greally,JohnM
动机为了了解基因组基因座组是否在一种或多种细胞类型的调控基因座富集，我们开发了gaiaAssociation软件包来进行调控景观富集分析（RLEA）。RLEA是一种新的分析过程，测试富集的基因组中的细胞类型特异性开放染色质区域（OCRs）的基因组。ResultsWe表明，RLEA的应用全基因组关联研究（GWAS）的数据揭示了细胞类型可能是介导的表型研究，和集群的OCRs的基础上共享的监管配置文件。GaiaAssociation是Python代码，可免费用于功能基因组学研究。可用性和实施Gaia Association可在PyPi（https：//pypi.org/project/gaiaAssociation/0.6.0/#description）上下载并在命令行或内联Python包中使用。Gaia Association也可以从GitHub安装，网址是https://github.com/GreallyLab/gaiaAssociation。
MotivationTo understand whether sets of genomic loci are enriched at the regulatory loci of one or more cell types, we developed the gaiaAssociation package to perform Regulatory Landscape Enrichment Analysis (RLEA). RLEA is a novel analytical process that tests for enrichment of sets of loci in cell type-specific open chromatin regions (OCRs) in the genome.ResultsWe demonstrate that the application of RLEA to genome-wide association study (GWAS) data reveals cell types likely to be mediating the phenotype studied, and clusters OCRs based on their shared regulatory profiles. GaiaAssociation is Python code that is freely available for use in functional genomics studies.Availability and ImplementationGaia Association is available on PyPi (https://pypi.org/project/gaiaAssociation/0.6.0/#description) for pip download and use on the command line or as an inline Python package. Gaia Association can also be installed from GitHub at https://github.com/GreallyLab/gaiaAssociation.