Differential Pathway Analysis

  • Jean FanEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1935)


Integrating prior knowledge of pathway-level information can enhance power and facilitate interpretation of gene expression data analyses. Here, we provide a practical demonstration of the value of gene set or pathway enrichment testing and extend such techniques to identify and characterize transcriptional subpopulations from single-cell RNA-sequencing data using pathway and gene set overdispersion analysis (PAGODA).

Key words

Single cell Pathway Gene set enrichment analysis Differential expression analysis Clustering 



This work was supported by NIH grant F99CA222750.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Chemistry and Chemical BiologyHarvard UniversityBostonUSA

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