StemDriver: a knowledgebase of gene functions for hematopoietic stem cell fate determination

StemDriver is a comprehensive knowledgebase dedicated to the functional annotation of genes participating in the determination of hematopoietic stem cell fate, available at http://biomedbdc.wchscu.cn/StemDriver/. By utilizing single-cell RNA sequencing data, StemDriver has successfully assembled a comprehensive lineage map of hematopoiesis, capturing the entire continuum from the initial formation of hematopoietic stem cells to the fully developed mature cells. Extensive exploration and characterization were conducted on gene expression features corresponding to each lineage commitment. At the current version, StemDriver integrates data from 42 studies, encompassing a diverse range of 14 tissue types spanning from the embryonic phase to adulthood. In order to ensure uniformity and reliability, all data undergo a standardized pipeline, which includes quality data pre-processing, cell type annotation, differential gene expression analysis, identification of gene categories correlated with differentiation, analysis of highly variable genes along pseudo-time, and exploration of gene expression regulatory networks. In total, StemDriver assessed the function of 23 839 genes for human samples and 29 533 genes for mouse samples. Simultaneously, StemDriver also provided users with reference datasets and models for cell annotation. We believe that StemDriver will offer valuable assistance to research focused on cellular development and hematopoiesis. Graphical Abstract

Automated summary

StemDriver is a comprehensive knowledgebase dedicated to annotating genes involved in determining the fate of hematopoietic stem cells. By analyzing single-cell RNA sequencing data, StemDriver has built a detailed lineage map of hematopoiesis, capturing the entire process from stem cell formation to mature cell development. The knowledgebase integrates data from 42 studies covering 14 tissue types, from embryonic to adult stages. Data undergo a standardized pipeline, including preprocessing, annotation, differential expression analysis, identification of differentiation-related gene categories, analysis of highly variable genes over pseudo-time, and exploration of gene regulatory networks. In total, StemDriver assesses the function of thousands of genes in human and mouse samples, and provides users with reference datasets and models for cell annotation.