Column Specifying the Immune Cell Types' Characteristic Genes

 
Creating Signatures:
Use All Genes   Dynamically Select a Subset
 

 
Show Results for:

      Cell Type Contrasts:
      Use Defaults
      Upload Your Own  

Perform Immune Cell Profiling:
Estimates immune cell abundance based on expression of immune cell-specific genes. Each cell type's abundance is estimated with the mean of its characteristic genes' expression. Cell type-specific genes are expected to be highly correlated and to predict each other's expression with a slope of 1; genes that do not match this pattern may be discarded.
 
Column Specifying the Immune Cell Types' Characteristic Genes:
Specifies the gene annotation column that identifies cell type specific genes.
 
Creating Signatures:
By default, cell type specific genes that do not mirror the expression of their counterparts will be removed before estimation of cell type abundance. Choosing the "Use All Genes" options skips this QC measure and uses all of a cell type's genes to measure its abundance.
 
P-value Threshold for Reporting Cell Type Abundance:
Defines the significance threshold for reporting a cell type abundance estimate. Cell types whose evidence for cell type-specific expression does not meet this level of evidence will be discarded. By default, this value is set to 1, returning results for all cell types regardless of how well their genes exhibit cell type-specific expression in your data. This choice relies on the accuracy of the literature around these genes (Bindea 2013). Choose a value of 0.05 or lower to only see results for cell types whose quantification is further supported by your data.
 
Show Results for:
Use these options to choose how expression activity abundance estimates are displayed.