Yan Shen, Chi Xu, Chang Xiao, Tian Mengliang
College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101300, China.
BMC Genomics. 2020 Oct 27;21(1):748. doi: 10.1186/s12864-020-07148-y.
Pathway analysis is widely applied in transcriptome analysis. Given certain transcriptomic changes, current pathway analysis tools tend to search for the most impacted pathways, which provides insight into underlying biological mechanisms. Further refining of the enriched pathways and extracting functional modules by "crosstalk" analysis have been proposed. However, the upstream/downstream relationships between the modules, which may provide extra biological insights such as the coordination of different functional modules and the signal transduction flow have been ignored.
To quantitatively analyse the upstream/downstream relationships between functional modules, we developed a novel GEne Set Topological Impact Analysis (GESTIA), which could be used to assemble the enriched pathways and functional modules into a super-module with a topological structure. We showed the advantages of this analysis in the exploration of extra biological insight in addition to the individual enriched pathways and functional modules.
GESTIA can be applied to a broad range of pathway/module analysis result. We hope that GESTIA may help researchers to get one additional step closer to understanding the molecular mechanism from the pathway/module analysis results.
通路分析在转录组分析中被广泛应用。给定特定的转录组变化，当前的通路分析工具倾向于寻找受影响最大的通路，这有助于深入了解潜在的生物学机制。有人提出通过“串扰”分析进一步细化富集通路并提取功能模块。然而，模块之间的上游/下游关系可能提供额外的生物学见解，如不同功能模块的协调和信号转导流程，却一直被忽视。
为了定量分析功能模块之间的上游/下游关系，我们开发了一种新颖的基因集拓扑影响分析（GESTIA），它可用于将富集通路和功能模块组装成具有拓扑结构的超级模块。我们展示了这种分析在探索除单个富集通路和功能模块之外的额外生物学见解方面的优势。
GESTIA可应用于广泛的通路/模块分析结果。我们希望GESTIA能帮助研究人员在从通路/模块分析结果理解分子机制方面更进一步。
