Welcome To Carcinoma EcoTyper

EcoTyper is a framework for the systematic identification of cell states and cellular communities (ecotypes) from bulk, single-cell and spatially-resolved gene expression data. This website allows users to explore features of the cell states and cellular communities identified in carcinoma samples from TCGA by EcoTyper, as well as recover cell states and ecotypes in user provided expression data.

Website features:

• Interact with, visualize, and explore EcoTyper results.
• Download data associated with the EcoTyper publication.
• Run EcoTyper to recover cell states and ecotypes on user provided bulk or scRNA-seq expression data.

The website does not allow users to discover new cell types and ecotypes in their own data, or perform cell state and ecotype recovery in spatial transcriptomics data. These functionalities are provided in the EcoTyper source code available in the Download section of this website and on the GitHub page of EcoTyper.

• Select a gene list, histology and cell type.
• This will display the expression signatures associated with all cell type specific states within this cancer type.
  • Hover or click and drag on the heatmap to explore genes and zoom.
  • To save time, the number of genes displayed per state is limited to 200. Download the full expression data to view all genes.
• Cell states across all cancer types may be displayed by selecting “Pan Carcinoma”.
• Core gene list is generated by CIBERSORTx in-silico purification. The extended gene lists is generated from a compendium of scRNA-seq datasets. The values displayed represent the average normalized expression across all scRNA-seq datasets.
• Users have the option to download:
  • The normalized expression matrix used to generate the heatmap.
  • A list of genes associated with a cell state of interest.
• The genes associated with a cell state of interest may be copied to the clipboard.

• Explore genes of interest and their expression across all cell states.
• Select a gene and a histology to display the expression of that gene in all cell states within the selected histology.
• An expression value of zero indicates that the gene was undetected in that cell state.

• This heatmap displays the association between cell state abundance and survival in TCGA.
• The associations are available as z-scores or directional -log10 P-values. Positive -log10 P-values indicate association with shorter survival, while negative values with longer survival.
• Explore the cell state expression signature for each association by clicking on the heatmap cells.

• This heatmap displays the association between carcinoma ecotypes abundance and survival in TCGA.
• The associations are available as z-scores or directional -log10 P-values. Positive -log10 P-values indicate association with shorter survival, while negative values with longer survival.
• Explore the cell state expression signature for each association by clicking on the heatmap cells.

• Explore the distribution of cell states and ecotypes across all cancer histologies.
• Select a cell type to display the frequency of each cell state in every cancer histology.
• Select a cell state to reorder the plot by the abundance of that cell state.
• The distribution of ecotypes may be viewed by selecting 'Ecotypes'

• Using this feature, ligand-receptor interactions between different cell types can be displayed, within and between ecotypes.
• Select the ecotypes of interest for ligands and receptors, then select the cell types whose ligands and receptors will be displayed.
• Use the button to download a csv file of the currently displayed data.
• See the downloads tab to download all ligand receptor interaction data for all ecotypes.