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. 2019 Sep 26:10:903.
doi: 10.3389/fgene.2019.00903. eCollection 2019.

SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes

Zishuai Wang  1 , Xikang Feng  1 , Shuai Cheng Li  1
Affiliations

SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes

Zishuai Wang et al. Front Genet. .

Erratum in

Abstract

Single-cell RNA-seq studies profile thousands of cells in developmental processes. Current databases for human single-cell expression atlas only provide search and visualize functions for a selected gene in specific cell types or subpopulations. These databases are limited to technical properties or visualization of single-cell RNA-seq data without considering the biological relations of their collected cell groups. Here, we developed a database to investigate single-cell gene expression profiling during different developmental pathways (SCDevDB). In this database, we collected 10 human single-cell RNA-seq datasets, split these datasets into 176 developmental cell groups, and constructed 24 different developmental pathways. SCDevDB allows users to search the expression profiles of the interested genes across different developmental pathways. It also provides lists of differentially expressed genes during each developmental pathway, T-distributed stochastic neighbor embedding maps showing the relationships between developmental stages based on these differentially expressed genes, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analysis results of these differentially expressed genes. This database is freely available at https://scdevdb.deepomics.org.

Keywords: cell type; database; development; differential expression; gene expression; single cell.

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Figures

Figure 1
Figure 1
The developmental tree. Figures of the brain, heart and digestion originate from Wikimedia Commons (https://commons.wikimedia.org/wiki/Main_Page).
Figure 2
Figure 2
Statistics of cell numbers of 35 developmental stages.
Figure 3
Figure 3
Overview of the gene expression search page. (A) Searching result of the gene “MYL2”. (B) Boxplot shows expression level distribution of MYL2 during developmental process by clicking the image. (C) The function of removing uninterested developmental stages by clicking the name of the stage listed in the figure legend. (D) An example of double clicking on a stage name.
Figure 4
Figure 4
Overview of the differential gene list collection page. (A). T-distributed stochastic neighbor embedding (t-SNE) maps showing the relationships between developmental stages based on these differentially expressed genes. (B). Top 20 Gene Ontology (GO) terms of differential expression genes. (C). Top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) terms of differential expression genes.
Figure 5
Figure 5
Comparison of MYL2 expression distributions between atrium cell types and ventricle cell types.
See this image and copyright information in PMC

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