Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns
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. Conside...
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Online Access: | http://dx.doi.org/10.1155/2017/3035481 |
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doaj-3c7352d5f9d643418766a92b360c9d7a2020-11-24T23:24:09ZengHindawi LimitedBioMed Research International2314-61332314-61412017-01-01201710.1155/2017/30354813035481Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression PatternsZhi Han0Travis Johnson1Jie Zhang2Xuan Zhang3Kun Huang4College of Software, Nankai University, Tianjin, ChinaDepartment of Biomedical Informatics, The Ohio State University, Columbus, OH, USADepartment of Biomedical Informatics, The Ohio State University, Columbus, OH, USACollege of Software, Nankai University, Tianjin, ChinaDepartment of Biomedical Informatics, The Ohio State University, Columbus, OH, USAWe 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.http://dx.doi.org/10.1155/2017/3035481 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Zhi Han Travis Johnson Jie Zhang Xuan Zhang Kun Huang |
spellingShingle |
Zhi Han Travis Johnson Jie Zhang Xuan Zhang Kun Huang Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns BioMed Research International |
author_facet |
Zhi Han Travis Johnson Jie Zhang Xuan Zhang Kun Huang |
author_sort |
Zhi Han |
title |
Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns |
title_short |
Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns |
title_full |
Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns |
title_fullStr |
Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns |
title_full_unstemmed |
Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns |
title_sort |
functional virtual flow cytometry: a visual analytic approach for characterizing single-cell gene expression patterns |
publisher |
Hindawi Limited |
series |
BioMed Research International |
issn |
2314-6133 2314-6141 |
publishDate |
2017-01-01 |
description |
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. |
url |
http://dx.doi.org/10.1155/2017/3035481 |
work_keys_str_mv |
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