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

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.

Author information

1
Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
2
Illumina Inc., San Diego, California, USA.
3
Department of Bioengineering, University of California, San Diego, California, USA.
4
Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California, USA.
5
Present address: AnchorDx Corporation, International Biotech Island, Guangzhou, Guangdong, China.

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.

PMID:
26780092
PMCID:
PMC4772672
DOI:
10.1038/nmeth.3734
[Indexed for MEDLINE]
Free PMC Article

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