PUBLICATION
ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells
- Authors
- Li, G., Luan, C., Dong, Y., Xie, Y., Zentz, S.C., Zelt, R., Roach, J., Liu, J., Qian, L., Li, Y., Yang, Y.
- ID
- ZDB-PUB-210828-39
- Date
- 2021
- Source
- International Journal of Molecular Sciences 22(16): (Journal)
- Registered Authors
- Liu, Jiandong
- Keywords
- R Shiny, cross-species comparison, differentially expressed genes, expressheart, non-cardiomyocytes, single-cell RNA-sequencing, visualization
- MeSH Terms
-
- Algorithms
- Animals
- Endothelial Cells/metabolism*
- Fibroblasts/metabolism*
- Gene Expression Profiling
- Heart Ventricles/metabolism*
- Humans
- Internet*
- Macrophages/metabolism*
- Mice
- Pericytes/metabolism*
- Sequence Analysis, RNA
- Single-Cell Analysis
- Software
- Transcriptome*
- Zebrafish
- PubMed
- 34445647 Full text @ Int. J. Mol. Sci.
Citation
Li, G., Luan, C., Dong, Y., Xie, Y., Zentz, S.C., Zelt, R., Roach, J., Liu, J., Qian, L., Li, Y., Yang, Y. (2021) ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells. International Journal of Molecular Sciences. 22(16):.
Abstract
Unveiling the molecular features in the heart is essential for the study of heart diseases. Non-cardiomyocytes (nonCMs) play critical roles in providing structural and mechanical support to the working myocardium. There is an increasing amount of single-cell RNA-sequencing (scRNA-seq) data characterizing the transcriptomic profiles of nonCM cells. However, no tool allows researchers to easily access the information. Thus, in this study, we develop an open-access web portal, ExpressHeart, to visualize scRNA-seq data of nonCMs from five laboratories encompassing three species. ExpressHeart enables comprehensive visualization of major cell types and subtypes in each study; visualizes gene expression in each cell type/subtype in various ways; and facilitates identifying cell-type-specific and species-specific marker genes. ExpressHeart also provides an interface to directly combine information across datasets, for example, generating lists of high confidence DEGs by taking the intersection across different datasets. Moreover, ExpressHeart performs comparisons across datasets. We show that some homolog genes (e.g., Mmp14 in mice and mmp14b in zebrafish) are expressed in different cell types between mice and zebrafish, suggesting different functions across species. We expect ExpressHeart to serve as a valuable portal for investigators, shedding light on the roles of genes on heart development in nonCM cells.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping