ARVEX

Select contrast

Select time zone

Select cell type

Show only TFs

Legends

Frq 1: Frequency of cells that the gene is detected in class 1

Frq 2: Frequency of cells that the gene is detected in class 2

BR time course

Enter gene ID (e.g. AT5G15150)

Search by gene name (e.g. HAT7)

Matched gene ID

Annotation

Cell type

Time zone

Visualization

Triangle plot

UMAP

Triangle plot annotation

Gene expression

Cell type

Time zone

Cell wall signature

Filtered by time zone (Triangle plot)

Fate 1 cell type (F1)

Fate 1 time zone (F1)

Fate 2 cell type (F2)

Fate 2 time zone (F2)

Cell type fate probability UMAP

Time zone fate probability UMAP

Cell wall signature UMAP

Opacity

Quantile cutoff

Notes and legends

Noticed that the fate probability calculation was anchored at BL 2 hour, that is why all the cells have either 0 or 1 probability

Arabidopsis Root Virtual Expression eXplorer

ARVEX is a Shiny app for exploring single cell gene expression of Arabidopsis root.

It hosts processed scRNA-seq data from Shahan and Hsu et al. 2022 and Nolan, Vukašinović and Hsu et al. 2022.

ARVEX features :

1. Singe cell gene expression in specific time zone and cell type. (See tab 'Gene expression')

2. Results of differential expression analysis for various contrasts. (See tab 'Differential expression')

3. Results of gene regulatory network analysis for Brassinosteroid time course. (See tab 'CellOracle ranked plot')

4. Results of stationary Waddington-OT analysis ( StationaryOT ) . (See tab 'Waddington-OT')

Data download links :

1. Raw data

For wild type atlas and shr scr mutant samples ( Shahan and Hsu et al. 2022 ), please refer to GEO : GSE152766

For BR samples ( Nolan, Vukašinović and Hsu et al. 2022 ), please refer to GEO : GSE212230

2. Annotations and normalized gene expression data

Can be downloaded here

Note, please consult the prefix of files for respective atlas :

'WT' for wild type atlas

'SHR' for shr scr mutant samples

'BR' for BR time course (includes Waddington-OT results in meta data)

'bri1-T' for bri1-T samples

'BRZ' for BRZ samples

'gtl1_df1' for gtl1 df1 samples

3. Results of differential expression analysis

Can be downloaded here

4. Results of GRN analysis (CellOracle)

Can be downloaded here for WT and BR time course

5. Codes for the analysis

Codes for Shahan and Hsu et al. 2022

Codes for Nolan, Vukašinović and Hsu et al. 2022

6. Input data for the analysis

CellOracle inputs can be downloaded here

WOT inputs can be downloaded here

7. SI data and tables for Nolan, Vukašinović and Hsu et al. 2022

Can be downloaded here

Contact:

ARVEX is developed and maintained by Che-Wei Hsu , please contact the author if you have questions.