Functional Virtual Flow Cytometry

A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns

Zhi Han, Travis Johnson, Jie Zhang, Xuan Zhang, Kun Huang

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

We presented a novel workflow for detecting distribution patterns in cell populations based on single-cell transcriptome study. With the fast adoption of single-cell analysis, a challenge to researchers is how to effectively extract gene features to meaningfully separate the cell population. Considering that coexpressed genes are often functionally or structurally related and the number of coexpressed modules is much smaller than the number of genes, our workflow uses gene coexpression modules as features instead of individual genes. Thus, when the coexpressed modules are summarized into eigengenes, not only can we interactively explore the distribution of cells but also we can promptly interpret the gene features. The interactive visualization is aided by a novel application of spatial statistical analysis to the scatter plots using a clustering index parameter. This parameter helps to highlight interesting 2D patterns in the scatter plot matrix (SPLOM). We demonstrated the effectiveness of the workflow using two large single-cell studies. In the Allen Brain scRNA-seq dataset, the visual analytics suggested a new hypothesis such as the involvement of glutamate metabolism in the separation of the brain cells. In a large glioblastoma study, a sample with a unique cell migration related signature was identified.

Original languageEnglish (US)
Article number3035481
JournalBioMed Research International
Volume2017
DOIs
StatePublished - Jan 1 2017
Externally publishedYes

Fingerprint

Flow cytometry
Gene expression
Flow Cytometry
Genes
Workflow
Gene Expression
Small Cytoplasmic RNA
Brain
Single-Cell Analysis
Cells
Spatial Analysis
Cell Separation
Gene Regulatory Networks
Glioblastoma
Transcriptome
Population
Cell Movement
Cluster Analysis
Glutamic Acid
Metabolism

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Functional Virtual Flow Cytometry : A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns. / Han, Zhi; Johnson, Travis; Zhang, Jie; Zhang, Xuan; Huang, Kun.

In: BioMed Research International, Vol. 2017, 3035481, 01.01.2017.

Research output: Contribution to journalArticle

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