SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes
SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes
复制标题
DOI：
10.3389/fgene.2019.00903
复制
发表时间：
2019-09-26
影响因子：
3.7
通讯作者：
Li, Shuai Cheng
中科院分区：
文献类型：
--
作者：
Wang, Zishuai;Feng, Xikang;Li, Shuai Cheng
单细胞rna-seq研究描述了数千个处于发育过程中的细胞。目前的人类单细胞表达图谱数据库只提供对特定细胞类型或亚群中选定基因的搜索和可视化功能。这些数据库仅限于单细胞RNA-SEQ数据的技术特性或可视化，而没有考虑其收集的细胞组的生物学关系。在这里，我们开发了一个数据库来研究单细胞基因在不同发育途径中的表达谱(SCDevDB)。在这个数据库中，我们收集了10个人类单细胞RNA-seq数据集，将这些数据集划分为176个发育细胞组，并构建了24条不同的发育途径。SCDevDB允许用户搜索不同发育途径上感兴趣的基因的表达谱。它还提供了每个发育途径中差异表达基因的列表，基于这些差异表达基因、基因本体论和京都基因百科全书以及这些差异表达基因的基因组分析结果，显示发育阶段之间关系的T分布随机邻居嵌入图。
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.