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BioMed Research International
Volume 2017, Article ID 3035481, 9 pages
Research Article

Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns

1College of Software, Nankai University, Tianjin, China
2Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
3The CCC Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH, USA

Correspondence should be addressed to Kun Huang; ude.cmuso@gnauh.nuk

Received 3 March 2017; Accepted 22 May 2017; Published 17 July 2017

Academic Editor: Ansgar Poetsch

Copyright © 2017 Zhi Han et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.