ExpressHeart

Welcome to our web browser, ExpressHeart! We present our analyses of five sets of single-cell RNA-sequencing datasets across three species, human, mouse and zebrafish. Feel free to explore those visualizations and download the differentially expressed genes. Please see the overview of ExpressHeart below.


How to cite:

If using ExpressHeart or the data provided, please cite:

Contact:

Comments, suggestions, questions are welcomed, and should be directed to Yuchen Yang (yyuchen@email.unc.edu) and Li Qian (li_qian@med.unc.edu). Please mention ExpressHeart by name to ensure avoiding spam detectors.

Acknowledgements

We would like to thank Dr. Li Wang, Dr. Hong Ma for their efforts in material preparation and data generation for Mouse-Wang-2021 and Zebrafish-Ma-2021 datasets, respectively, and Duan Wang and Hanling Wang for their assistance in the cartoon illustration on ExpressHeart. We also want to thank all the Qian and Liu Lab members for feedback on ExpressHeart. We would like to thank the Nordon, Harvey, Pinto, Ren, Chi and Preissl Labs for generating those scRNA-seq/snRNA-seq datasets incorporated in ExpressHeart.

The Human-Hocker-2021 dataset comprises of 8,993 nonCM cells from the hearts of two healthy adult human donors. Nine cell types were identified, including fibroblasts, myofibroblasts, endothelial cells, pericytes, adipocytes, smooth muscle cells, nerve cells and two groups of immune cells (macrophages and lymphocytes).


Figure Download

Please enter the gene's (or genes') names:

Notes: Example of inputting format: DCN

Please choose the cell types:



Figure Download

Please enter a gene's name:

Notes: (1) Example of inputting format: DCN
(2) Only one gene's name is acceptable at one time




Figure Download

Please upload a txt file including the genes'names:

Notes: (1) Only one gene's name is acceptable in each row in the txt file.
(2) With no puctuations between genes




Figure Download

The mouse dataset from Wang et al. (Cardiovascular Research, 2021, PMID: 33839759) consists of 12,779 cells from two adult mice, encompassing six major nonCM cell types, namely fibroblasts, endothelial cells, pericytes, granulocytes and two types of immune cells (macrophages and lymphocytes). Of them, the three major cell types (fibroblasts, endothelial cells and macrophages) are further clustered into three to five subtypes with each subtype representing a distinct functional state.


Figure Download

Please enter the gene's (or genes') names:

Notes: Example of inputting format: Tcf21,Cdh5

Please choose the cell types:



Figure Download

Please enter a gene's name:

Notes: (1) Example of inputting format: Tcf21
(2) Only one gene's name is acceptable at one time.




Figure Download

Please upload a txt file including the genes'names:

Notes: (1) Only one gene's name is acceptable in each row in the txt file.
(2) With no puctuations between genes.




Figure Download

Table Download:Fibroblast

Press the linking buttons below to transfer to the subcluster tables.


Table Download:Macrophage

Press the linking buttons below to transfer to the subcluster tables.



Table Download:Endothelial cells

Press the linking buttons below to transfer to the subcluster tables.



The mouse dataset from Farbehi et al. (Elife, 2019, PMID: 30912746) is comprised of 12,991 nonCM cells (the total cardiac interstitial cell population (TIP)) from healthy and injured mouse hearts (3 and 7 days post-MI surgery), where 5,658, 3,825 and 3,508 cells are from healthy, 3 days post-MI and 7 days post MI hearts, respectively. Unbiased clustering identified 24 cell populations, including the major cell types fibroblasts, endothelial cells, mural cells and immune cells (macrophages, monocytes, dendritic cells, B cells, T cells and natural killer (NK) cells). Similarly, there are multiple subtypes identified for several major cell types. For example, four subtypes are identified in fibroblasts; three in endothelial cells, and eight in macrophages/monocytes.





Figure Download

Please enter the gene's (or genes') names:

Notes: Example of inputting format: Tcf21,Cdh5

Please choose the cell types:



Figure Download

Please enter a gene's name:

Notes: (1) Example of inputting format: Tcf21
(2) Only one gene's name is acceptable at one time.




Figure Download

Please upload a txt file including the genes'names:

Notes: (1) Only one gene's name is acceptable in each row in the txt file.
(2) With no puctuations between genes.




Figure Download

Table Download:Fibroblast

Press the linking buttons below to transfer to the subcluster tables.



Table Download:Macrophage

Press the linking buttons below to transfer to the subcluster tables.






Table Download:Endothelial cells

Press the linking buttons below to transfer to the subcluster tables.


The Mouse-McLellan-2020 dataset (PMID: 32795101) comprises of 13,176 nonCM cells from four un-treated, four sham- and eight AngII-treated adult mice, where angiotensin II-treatment could stimulate pathological remodeling of heart. A total of 14 cell types were identified, including fibroblasts, epicardial cells, endothelial cells, lymphatic endothelial cells, endocardial cells, smooth muscle cells, pericytes, schwann cells, proliferating mesenchymal cells, macrophages, dendritic-like cells, granulocytes, B cells and T/NK cells. In addition, nine, three, four and two subtypes were identified for the major cell types, fibroblasts, endothelial cells, macrophages and smooth muscle cells, respectively.


Figure Download

Please enter the gene's (or genes') names:

Notes: Example of inputting format: Tcf21,Cdh5

Please choose the cell types:



Figure Download

Please enter a gene's name:

Notes: (1) Example of inputting format: Tcf21
(2) Only one gene's name is acceptable at one time.




Figure Download

Please upload a txt file including the genes'names:

Notes: (1) Only one gene's name is acceptable in each row in the txt file.
(2) With no puctuations between genes.




Figure Download

Table Download:Fibroblasts

Press the linking buttons below to transfer to the subcluster tables.








Table Download:Macrophages

Press the linking buttons below to transfer to the subcluster tables.



Table Download:Endothelial cells

Press the linking buttons below to transfer to the subcluster tables.


The zebrafish dataset from Ma et al. (unpublished) consists of 25,972 cells from healthy and injured zebrafish hearts. The authors performed scRNA-seq on the nonCMs isolated from the adult zebrafish hearts before and after injury to investigate cellular functions of nonCMs during heart regeneration. The study generated transcriptome profiles for 6,550, 9,373, 7,018 and 3,031 cells before injury (uninjured heart), and at 2, 7 and 14 days post-injury, respectively. Nine clusters were identified in the uninjured hearts , namely fibroblasts, endothelial cells, thrombocytes and six types of immune cells (macrophages, neutrophils, resident mesenchymal cells, T cells, B cells, and NK cells). Integrative analysis was performed for each of the three major cell types, fibroblasts, endothelial cells and macrophages, and further identified four, four and five subtypes, respectively.


Figure Download

Please enter the gene's (or genes') names:

Notes: Example of inputting format: tcf21,cdh5

Please choose the cell types:



Figure Download

Please enter a gene's name:

Notes: (1) Example of inputting format: tcf21
(2) Only one gene's name is acceptable at one time




Figure Download

Please upload a txt file including the genes'names:

Notes: (1) Only one gene's name is acceptable in each row in the txt file.
(2) With no puctuations between genes




Figure Download

Table Download:FB

Press the linking buttons below to transfer to the subcluster tables.



Table Download:Macrophage

Press the linking buttons below to transfer to the subcluster tables.




Table Download:Endothelial cells

Press the linking buttons below to transfer to the subcluster tables.



ExpressHeart incorporates multiple datasets from three species, thus allowing users to perform the analyses of nonCMs features between different datasets from the same species, as well as across different species. These analyses can provide a comprehensive view of the similarities and differences in the transcriptomic dynamics among different conditions or different species.


We first provide a panel “DEG Query” allowing users to check whether a gene of interests is differentially expressed in any of the four incorporating datasets. For a given gene, if it is a DEG, ExpressHeart would list all the relevant information, including differentially expressing in which cell type and dataset, the proportions of cells the gene detected in the target and background cell groups and the adjusted p-value.


Second, we provide lists of high confidence DEGs. For scRNA-seq data, cluster annotation largely depends on the prior knowledge on the expression profiles of cell type-specific features. A comprehensive list of genes differen-tially expressed among cell types can improve the accuracy for cell type discovery. However, although there are a large amount of scRNA-seq data available, different datasets are generally generated from different laboratories, using different techniques, and/or under different conditions, and the DEGs identified in different datasets are usually different. With the help of ExpressHeart, we can obtain a confident list of DEGs for a certain cell type across multiple datasets.


For the cross-species distribution comparison between mouse and zebrafish, the uninjured zebrafish cells from Zebrafish-Ma-2021 were first extracted, and then compared with the wildtype mouse cells from Mouse-Wang-2021. Only genes having mouse-zebrafish homologs are visualized in ExpressHeart.


Please enter a gene's name:

Notes: (1) Example of inputting format: Mmp14
(2) Only one gene's name is acceptable at one time
Table Download
Note: The choice of Three Major Cell Types includes Fibroblasts, Endothelial cells and Macrophages.

High Confidence DEGs Download Figure Download

Below is the upset plot of DEGs for the chosen major cell types across two mouse datasets.

Please enter a gene's name:

Notes: (1) Example of inputting format: mmp14b
(2) Only one gene's name is acceptable at one time
Figure Download

Mouse Violin Plot

Fish Violin Plot

Human Violin Plot

Here we provided results from differential expression analysis among different cell types, as well as among different subtypes within each of the three major cell types, fibroblasts, endothelial cells and macrophages.The Human-Hocker-2021 dataset only contains expression information in major clusters.

DEGs of Human-Hocker-2021 (size:153k)

DEGs of Human-Hocker-2021

DEGs of Mouse-Wang-2021 (size:263k)

DEGs of Mouse-Wang-2021

DEGs of Mouse-Farbehi-2019 (size:551k)

DEGs of Mouse-Farbehi-2019

DEGs of Mouse-McLellan-2020 (size:654k)

DEGs of Mouse-McLellan-2020

DEGs of Zebrafish-Ma-2021 (size:310k)

DEGs of Zebrafish-Ma-2021

Using ExpressHeart

The goal of our web portal ExpressHeart is to provide a user-friendly platform for visualizing and analyzing the transcriptome profiles of cardiac nonCMs. ExpressHeart currently incorporates four scRNA-seq datasets, namely, Human-Hocker-2021,Mouse-Wang-2021, Mouse-Farbehi-2019 and Zebrafish-Ma-2021.

1. Home

This panel provides a basic introduction.

2. Human-Hocker-2021

The structure and content are similiar with the tab of '3. Mouse-Wang-2021'.

3. Mouse-Wang-2021

This panel corresponds to the analysis results of Mouse-Wang-2021 data, including seven sub-panels.


3.1 Introduction

This panel provides a basic introduction to Mouse-Wang-2021 data.


3.2 2D Visualization

A: Choose the dimention-reducting method.

B: Download the UMAP/tSNE plot.

C: Present the UMAP/tSNE plot.


3.3 Gene Violin Plot

A: Input the genes' names for violin plot.

B: Choose the cell types if users want to check a more comprehensive view of the distribution of gene expression across these choosen cell types.

C: Click this submit button to generate the violin plot.

D: Download the violin plot.

E: Present the violin Plot.


3.4 Gene Feature Plot

A: Input the gene's name for violin plot. Only one gene's name is accepted at one time.

B: Choose the dimention-reducting method.

C: This is the submit button. After inputting the gene's name and selecting a dimention-reducting method, you need to press this button, then the feature plot will be shown on the right area.

D: Download the gene feature plot.

E: Present the gene feature plot.


3.5 Gene Heatmap Plot

A: Upload a txt file as input from users' local computer. The txt file should contain the genes' names of user's interests. In the txt file, each row must contain only one gene's name without any puctuations between rows.

B: Submit button. After inputting a txt file, you need to press this button, then the heatmap plot will be shown on the right.

C: Download the heatmap plot.

D: Present the heatmap plot.


3.6 DEGs for Major Clusters

A: This is a tab through which you can choose a major cell type to check the results of the differencial expression analysis.

B: Present the DEGs.

C: This is the area displaying UMAP/t-SNE) plot highlighting the target cell type in color (while the other cell types are in grey).

D: Download the table.

E: Links to the DEGs tables for the corresponding subtypes.


3.7 DEGs for Sub-clusters

A: Choose one of three major cell types: Firoblast, Macrophage, and Endothelial cell.

B: Present DEGs of a choosen subtype.

C: This is the area displaying the UMAP/t-SNE) plot highlighting the target subtype within it's major cell type.

D: Download the table.

4. Mouse-Farbehi-2019

The structure and content are similiar with the tab of '2. Mouse-Wang-2021'.

5. Mouse-McLellan-2020

The structure and content are similiar with the tab of '2. Mouse-Wang-2021'.

6. Zebrafish-Ma-2021

The structure and content are similiar with the tab of '2. Mouse-Wang-2021'.

7. Cross Comparision


7.1 Introduction

This panel provides a basic introduction to the Cross Comparision panel.


7.2 DEG Query

A: This blank is used to input the gene's name to to query it's expressing information in every dataset.

B: This is the submit button. After inputting the gene's name, you need to press this button, then the corresponding plot will be shown on the right.

C: This is a download button providing to download the table.

D: This area displays the query result.


7.3 High Confidence DEGs

A: Choose the major cell type to check it's upset plot across two mouse datasets.

B: This area displays upset plots of DEGs for the chosen major cell types across two mouse datasets.

C: This is a download button providing to download high confidence DEGs.

D: This is a download button providing to download the upset plot.


7.4 Cross-species Distribution Comparion

A: This blank is used to input the gene's name for violin plots in different species. Only one gene's name is accepted at one time.

B: This is the submit button. After inputting the gene's name, you need to press this button, then the corresponding plot will be shown on the right.

C: This is a download button providing to download the comparision violin plots.

D: This area displays violin plots of homolog genes in different species.

8. Download

This panel provide three dowanload buttons for users to download the DEGs for each dataset.