Using ICLite for deconvolution of bulk transcriptional data from mixed cell populations.
Using ICLite for deconvolution of bulk transcriptional data from mixed cell populations.
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DOI：
10.1016/j.xpro.2021.100847
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发表时间：
2021-12-17
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影响因子：
--
通讯作者：
Ray A
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文献类型：
--
作者：
Camiolo MJ;Wenzel SE;Ray A
来自异质细胞群体的大量表达数据对研究人员提出了挑战，因为细胞数量和转录程序的差异可能使分析复杂化。为了提高混合群体批量RNA测序的性能，我们通过探索性矩阵创建了免疫细胞连锁（ICLite）。用于R的ICLite软件包构建了相关基因的模块，并确定了它们与混合细胞群体中特定谱系的关系。本方案详细说明了ICLite实施后的格式、运行参数优化和结果解释。有关本方案使用和执行的完整详细信息，请参阅。ICLite识别来自混合细胞群的批量转录数据中的基因模块协议详细说明了如何运行和解释ICLite的结果参数调整、数据格式和解决方案评估的讨论运行后探索的细节，包括基因本体和语义相似性来自异质细胞群的批量表达数据对研究人员构成了挑战，因为细胞数量和转录程序的差异可能使分析复杂化。为了提高混合群体批量RNA测序的性能，我们通过探索性矩阵创建了免疫细胞连锁（ICLite）。用于R的ICLite软件包构建了相关基因的模块，并确定了它们与混合细胞群体中特定谱系的关系。本方案详细说明了ICLite实施后的格式、运行参数优化和结果解释。
Bulk expression data from heterogeneous cell populations pose a challenge for investigators, as differences in cell numbers and transcriptional programs may complicate analysis. To improve the performance of bulk RNA sequencing on mixed populations, we created Immune Cell Linkage through Exploratory Matrices (ICLite). The ICLite package for R constructs modules of correlated genes and identifies their relationship to specific lineages in mixed cell populations. This protocol details formatting, optimization of run parameters, and interpretation of results following implementation of ICLite. For complete details on the use and execution of this protocol, please refer to. ICLite identifies gene modules in bulk transcriptional data from mixed cell populations Protocol details how to run and interpret the results of ICLite Discussion of parameter tuning, data formatting, and solution evaluation Details for post-run exploration including gene ontology and semantic similarity Bulk expression data from heterogeneous cell populations pose a challenge for investigators, as differences in cell numbers and transcriptional programs may complicate analysis. To improve the performance of bulk RNA sequencing on mixed populations, we created Immune Cell Linkage through Exploratory Matrices (ICLite). The ICLite package for R constructs modules of correlated genes and identifies their relationship to specific lineages in mixed cell populations. This protocol details formatting, optimization of run parameters, and interpretation of results following implementation of ICLite.
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