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Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

Academic Article
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Overview

authors

  • Fan, J.
  • Salathia, N.
  • Liu, R.
  • Kaeser, G. E.
  • Yung, Y. C.
  • Herman, J. L.
  • Kaper, F.
  • Fan, J. B.
  • Zhang, K.
  • Chun, Jerold
  • Kharchenko, P. V.

publication date

  • March 2016

journal

  • Nature Methods  Journal

abstract

  • 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.

subject areas

  • Animals
  • Cells, Cultured
  • Computer Simulation
  • Gene Expression Profiling
  • Mice
  • Models, Biological
  • Models, Statistical
  • Neurons
  • Proteome
  • Sequence Analysis, RNA
  • Signal Transduction
  • Transcription, Genetic
  • Transcriptome
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Identity

PubMed Central ID

  • PMC4772672

International Standard Serial Number (ISSN)

  • 1548-7091

Digital Object Identifier (DOI)

  • 10.1038/nmeth.3734

PubMed ID

  • 26780092
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Additional Document Info

start page

  • 241

end page

  • 244

volume

  • 13

issue

  • 3

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