Average Expression per Cluster






Normalized cluster expression - leaf.cluster-expression-norm.txt
Raw cell x gene expression matrix - leaf.expression-matrix-raw.txt.gz
Lightweight Seurat object - leaf.RDS



Average Expression per Cluster






Normalized cluster expression - leaf.cluster-expression-norm.txt
Raw cell x gene expression matrix - vasculature.expression-matrix-raw.txt.gz
Lightweight Seurat object - vasculature.RDS

User Manual


1. Provided Datasets



2. Querying Genes

  • The genes can be queried using the text input box on the left panel. Up to 30 comma-separated genes can be queried.
  • Alternatively, the user can upload a simple .txt file containing one gene per line.
  • The input can be provided as TAIR IDs (AT5G15290…) or using common names (SHR, SCR…). However, only TAIR IDs will be reported in the output plots.
  • In some cases, common names can refer to multiple unique TAIR IDs (ATM1, ARF3…). In such cases, please use TAIR IDs instead.
  • Please note that querying a large number of genes can lead to slow data processing.
  • The expression of some genes is altered during the single-cell library preparation as a cell response to the protoplasting process (protoplasting-induced genes). If the queried genes were identified as significantly affected, a warning (yellow) will be displayed in the bottom-right screen corner. Yet, querying such genes can still deliver informative results.
  • If the queried genes are not present in the dataset, an error notification (red) will be displayed in the bottom-right screen corner, and the gene will not appear in the output plot.



3. Feature Plot

  • The feature plot shows gene expression of individual cells (dots) projected on a UMAP visualization. A more intense red color means a higher normalized expression.
  • Each plot has an individual scale. Therefore, the expression levels of individual genes cannot be directly compared using the color intensities without considering the scale bar.
  • For interpretation of observed expression patterns, please refer to the cluster annotation on the left panel.



4. Expression level

  • The violin plots show the normalized gene expression of the cells (dots) within individual clusters.
  • In the case of lowly expressed genes, the violin plots can look like lines. This is an expected behavior due to many cells (dots) accumulated at zero values.
  • The average expression levels per cluster are reported in the ‘Average expression’ table.



6. Data Download

  • Normalized cluster expression – A file containing normalized average expression values per cluster.
  • Raw cell x gene expression matrix – A matrix containing raw counts in a cell x gene format. This can be used for the atlas/trajectory reconstruction.
  • Lightweight Seurat object – a Seurat object containing normalized scaled expression values. Additionally, cell identity information and pseudotime values are stored here. It can be used for visualization purposes.



7. Citation



8. Contact

  • If you have any questions, please contact: marja.timmermans@zmbp.uni-tuebingen.de
  • If you wish to report a bug in the browser, please contact Pavel Solanský: pavel.solansky@zmbp.uni-tuebingen.de

  • Timmermans Lab