This function allows users to keep samples in the sub-datasets (tissues from GTEx or cancer types from TCGA) they selected, and filter the cell types of interest to visualize and compare their proportions in each bulk sample. Up to five sub-datasets are supported.

After clicking the "plot" button, the interactive boxplots grouped by cell type and sub-dataset will be available. The one-way ANOVA function has been dynamically integrated into each sub-group in each boxplot, allowing users to have a quantitative comparison of the cell proportions.

Parameters

  • TCGA Tumor/TCGA Normal/GTEx/Used Expression Datasets: Select cancer types of interest in the "TCGA Tumor", "TCGA Normal" or "GTEx" field and click "add" to build dataset list in the "Used Expression Datasets" field. Also, manual input of cancer types split by comma (e.g. COAD Tumor,READ Tumor) is also acceptable. The cell type proportion analysis is based on the datasets list.
  • Cell Types: Select cell types of interest for analysis.
  • Normalization: For each sample, normalize the proportions of selected cell types to make the sum equal to 1.

--- Help ---

Add
Add
Add
Select deconvolution tool:
CIBERSORT EPIC quanTIseq
Cell types:
B.cells.naive
B.cells.memory
Plasma.cells
T.cells.CD8
T.cells.CD4.naive
T.cells.CD4.memory.resting
T.cells.CD4.memory.activated
T.cells.follicular.helper
T.cells.regulatory..Tregs.
T.cells.gamma.delta
NK.cells.resting
NK.cells.activated
Monocytes
Macrophages.M0
Macrophages.M1
Macrophages.M2
Dendritic.cells.resting
Dendritic.cells.activated
Mast.cells.resting
Mast.cells.activated
Eosinophils
Neutrophils
B Cells
CD4 T cells
CD8 T cells
NK cells
Macrophages
Endothelials
Cancer associated fibroblasts
Other Cells
B cell
Macrophage M1
Macrophage M2
Monocyte
Neutrophil
NK cell
T cell CD4+ (non-regulatory)
T cell CD8+
T cell regulatory (Tregs)
Myeloid dendritic cell
uncharacterized cell

Normalization: True False
Reset The plot is based on the datasets of list.