可视化
追踪
代谢组学
聚类分析
化学
计算生物学
计算机科学
数据挖掘
注释
集合(抽象数据类型)
数据可视化
特征选择
人工智能
色谱法
操作系统
生物
程序设计语言
作者
Lichuang Huang,Qiyuan Shan,Qiang Lyu,Shuosheng Zhang,Lu Wang,Gang Cao
标识
DOI:10.1021/acs.analchem.3c01072
摘要
Untargeted mass spectrometry is a robust tool for biology, but it usually requires a large amount of time on data analysis, especially for system biology. A framework called Multiple-Chemical nebula (MCnebula) was developed herein to facilitate the LC-MS data analysis process by focusing on critical chemical classes and visualization in multiple dimensions. This framework consists of three vital steps as follows: (1) abundance-based classes (ABC) selection algorithm, (2) critical chemical classes to classify "features" (corresponding to compounds), and (3) visualization as multiple Child-Nebulae (network graph) with annotation, chemical classification, and structure. Notably, MCnebula can be used to explore the classification and structural characteristic of unknown compounds beyond the limit of the spectral library. Moreover, it is intuitive and convenient for pathway analysis and biomarker discovery because of its function of ABC selection and visualization. MCnebula was implemented in the R language. A series of tools in R packages were provided to facilitate downstream analysis in an MCnebula-featured way, including feature selection, homology tracing of top features, pathway enrichment analysis, heat map clustering analysis, spectral visualization analysis, chemical information query, and output analysis reports. The broad utility of MCnebula was illustrated by a human-derived serum data set for metabolomics analysis. The results indicated that "Acyl carnitines" were screened out by tracing structural classes of biomarkers, which was consistent with the reference. A plant-derived data set was investigated to achieve a rapid annotation and discovery of compounds in E. ulmoides.
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