Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.
Jean FanNeeraj SalathiaRui LiuGwendolyn E KaeserYun C YungJoseph L HermanFiona KaperJian-Bing FanKun ZhangJerold ChunPeter V KharchenkoPublished in: Nature methods (2016)
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.
Keyphrases
- single cell
- rna seq
- cell cycle
- high throughput
- gene expression
- copy number
- genome wide
- transcription factor
- cell proliferation
- induced apoptosis
- genome wide identification
- stem cells
- heat shock
- electronic health record
- endoplasmic reticulum stress
- cerebral ischemia
- bone marrow
- oxidative stress
- blood brain barrier
- cell death