Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

Nat Methods. 2016 Mar;13(3):241-4. doi: 10.1038/nmeth.3734. Epub 2016 Jan 18.


The transcriptional state of a cell reflects a variety of biological factors, from cell-type-specific features to transient processes such as the cell cycle, all of which may be of interest. However, identifying such aspects from noisy single-cell RNA-seq data remains challenging. We developed pathway and gene set overdispersion analysis (PAGODA) to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Cells, Cultured
  • Computer Simulation
  • Gene Expression Profiling / methods*
  • Mice
  • Models, Biological
  • Models, Statistical
  • Neurons / physiology
  • Proteome / chemistry
  • Proteome / metabolism*
  • Sequence Analysis, RNA / methods*
  • Signal Transduction / physiology*
  • Transcription, Genetic / physiology*
  • Transcriptome / physiology*


  • Proteome