Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

Elife. 2019 Jul 8;8:e43803. doi: 10.7554/eLife.43803.


Identifying gene expression programs underlying both cell-type identity and cellular activities (e.g. life-cycle processes, responses to environmental cues) is crucial for understanding the organization of cells and tissues. Although single-cell RNA-Seq (scRNA-Seq) can quantify transcripts in individual cells, each cell's expression profile may be a mixture of both types of programs, making them difficult to disentangle. Here, we benchmark and enhance the use of matrix factorization to solve this problem. We show with simulations that a method we call consensus non-negative matrix factorization (cNMF) accurately infers identity and activity programs, including their relative contributions in each cell. To illustrate the insights this approach enables, we apply it to published brain organoid and visual cortex scRNA-Seq datasets; cNMF refines cell types and identifies both expected (e.g. cell cycle and hypoxia) and novel activity programs, including programs that may underlie a neurosecretory phenotype and synaptogenesis.

Keywords: brain organoids; computational biology; gene expression programs; genetics; genomics; human; matrix factorization; mouse; single-cell Rna-Seq; synaptogenesis; systems biology; visual cortex.

Publication types

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

MeSH terms

  • Algorithms
  • Animals
  • Brain / cytology
  • Brain / metabolism*
  • Computer Simulation
  • Gene Expression Profiling / methods*
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Mice
  • Models, Genetic
  • Organoids / cytology
  • Organoids / metabolism
  • RNA-Seq / methods*
  • Reproducibility of Results
  • Single-Cell Analysis / methods*
  • Visual Cortex / cytology
  • Visual Cortex / metabolism*

Associated data

  • GEO/GSE86153
  • GEO/GSE102827
  • GEO/GSE71585
  • GEO/GSE50244