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.
Warning: A non-default cell type gene annotation column has been selected, which may interfere with calculation of relative cell type abundance.
Calculation of relative cell abundance relies on a .csv file specifying a "cell type contrasts matrix". The default cell type contrasts matrix assumes that the default cell type gene annotation column has been used. Use of a custom cell type gene annotation column may limit the utility of the default cell type contrasts matrix: new cell type names will not yield relative cell type abundance results, and removed cell type names will eliminate their associated cell type contrasts.
The default cell type contrasts matrix uses the following raw cell type measurements:
- B-cells
- CD4 activated
- CD8 T-cells
- Cytytoxic cells
- DC
- Macrophages
- Mast cells
- Neutrophils
- NK cells
- Normal mucosa
- T-cells
- T helper cells
- Th1 cells
- Th2 cells
- Treg
To calculate the following contrasts:
- B-cells,CD8 vs Treg
- CD8 vs Tcells
- T helpers vs T cells
- Mast cells norm
- CD8 vs CD4
- CD8 vs cytotoxic
- DC,NK,Th1 vs Th2